Open sum732 opened 2 years ago
Hmm, there seems to be a problem earlier, "collating 0 samples" feels like an item of concern. I'm not sure if it is a potential mismatch in column headings for the sgRNA in Count_Matrix.tab vs sgrna [all lower case] in sgRNA_Mapping_File , or ability to identify the sample from sample file. The way in which the replicate and sample are specified has been improved over the years, so I am not completely sure what the right encoding is, but I would think it to potentially be the main culprit. Let me know if this does not help rapidly resolve,
Leo
On Tue, Nov 9, 2021 at 11:24 PM sum732 @.***> wrote:
Hello, I am trying to use JACKS and running into following issues:
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File.tab --sgrna_hdr=sgrna --gene _hdr=Gene --ctrl_sample_hdr=Sample --outprefix JACKS [2021-11-09 18:05:01,363] jacks: INFO Loading sample specification [2021-11-09 18:05:01,363] jacks: INFO Loading gene mappings [2021-11-09 18:05:01,365] jacks: INFO Loading data and pre-processing [2021-11-09 18:05:01,424] jacks: INFO Applying median normalisation [2021-11-09 18:05:01,471] jacks: INFO Collating 0 samples [2021-11-09 18:05:01,487] jacks: INFO Running JACKS inference /home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice return fun(*args, kwargs) /home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice. LOG.debug("After init, mean absolute error=%.3f,
=%.1f 2)0.5), w1.mean(), SP.median((w2-w12)*0.5), x1.mean()w1.mean())) /home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, [2021-11-09 18:05:01,801] jacks: INFO Writing JACKS results /gpfs/fs1/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results] /home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]=%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound)) /home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount) /home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice. LOG.debug("After W update, =%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean())) /home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice. LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x1 Here are snippets of how various files look: head -n +4 Count_Matrix.tab
sgRNA P23H1 P23H2 Control1 Control2 Control3 Amfr_sgRNA1 150 44 602 530 302 Amfr_sgRNA2 141 24 380 350 162 Amfr_sgRNA3 203 21 443 435 303
head Exp_Summary_JACKS.tab
Replicate Sample P23H1 P23H P23H2 P23H Control1 CTRL Control2 CTRL Control3 CTRL
head -n +3 sgRNA_Mapping_File.tab
sgrna Gene Sec24d_sgRNA2 Sec24d Gm30534_sgRNA3 Gm30534
Not exactly why any array slice will produce a mean of <0( assuming that is the error). The counts is tab separated and so are the other files as well.
Any help will be much appreciated.
Thanks, D
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/felicityallen/JACKS/issues/17, or unsubscribe https://github.com/notifications/unsubscribe-auth/AADIQI6XOACLLJVE747LUE3ULGUQ7ANCNFSM5HWQIMGA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
Hi Leo, Thank you for responding and for the suggestion. I had tried setting things correctly
head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab
==> Count_Matrix-Fixed.tab <==
sgrna Gene P23H_rep1 P23H_rep2 Control_rep1 Control_rep2 Control_rep3
==> sgRNA_Mapping_File-Fixed.tab <==
sgrna Gene
Got this error
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgrna --gene_h
dr=Gene --ctrl_sample_hdr=Sample --outprefix JACKS
[2021-11-11 17:39:54,074] jacks: INFO Loading sample specification
[2021-11-11 17:39:54,075] jacks: INFO Loading gene mappings
[2021-11-11 17:39:54,078] jacks: INFO Loading data and pre-processing
[2021-11-11 17:39:54,136] jacks: INFO Applying median normalisation
[2021-11-11 17:39:54,184] jacks: INFO Collating 0 samples
[2021-11-11 17:39:54,200] jacks: INFO Running JACKS inference
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice
return fun(*args, **kwargs)
/homes/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice.
LOG.debug("After init, mean absolute error=%.3f, <x>=%.1f <w>=%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound))
/gpfs/fs1/home/mehrotras/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice.
LOG.debug("After W update, <w>=%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean()))
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice.
LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x1**2)**0.5), w1.mean(), SP.median((w2-w1**2)**0.5), x1.mean()*w1.mean()))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
[2021-11-11 17:39:54,511] jacks: INFO Writing JACKS results
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
(jacksenv) mehrotras@login01:$/JACKS>head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab
Changed to Match
head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab
==> Count_Matrix-Fixed.tab <==
sgRNA Gene P23H_rep1 P23H_rep2 Control_rep1 Control_rep2 Control_rep3
==> sgRNA_Mapping_File-Fixed.tab <==
sgRNA Gene
Error
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgRNA --gene_hdr=Gene --ctrl_sample_hdr=Sample --outprefix JACKS
[2021-11-11 17:42:37,162] jacks: INFO Loading sample specification
[2021-11-11 17:42:37,162] jacks: INFO Loading gene mappings
[2021-11-11 17:42:37,164] jacks: INFO Loading data and pre-processing
[2021-11-11 17:42:37,223] jacks: INFO Applying median normalisation
[2021-11-11 17:42:37,272] jacks: INFO Collating 0 samples
[2021-11-11 17:42:37,288] jacks: INFO Running JACKS inference
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice
return fun(*args, **kwargs)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice.
LOG.debug("After init, mean absolute error=%.3f, <x>=%.1f <w>=%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice.
LOG.debug("After W update, <w>=%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean()))
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice.
LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x1**2)**0.5), w1.mean(), SP.median((w2-w1**2)**0.5), x1.mean()*w1.mean()))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
[2021-11-11 17:42:37,602] jacks: INFO Writing JACKS results
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
Here is Expsummary
cat Exp_Summary_JACKS.tab
Replicate Sample
P23H_rep1 P23H
P23H_rep2 P23H
Control_rep1 CTRL
Control_rep2 CTRL
Control_rep3 CTRL
These all are tab separated, I reconfirmed this.
Just to triple check - did you use the latest version, and have you tried explicitly setting --rep_hdr=Replicate --sample_hdr=Sample ? The --ctrl-sample-hdr is for the third header, I worry if the defaults for first two match what you use. https://github.com/felicityallen/JACKS/tree/master/jacks has the example
On Thu, Nov 11, 2021 at 10:50 PM sum732 @.***> wrote:
Hi Leo, Thank you for responding and for the suggestion. I had tried setting things correctly
head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab ==> Count_Matrix-Fixed.tab <== sgrna Gene P23H_rep1 P23H_rep2 Control_rep1 Control_rep2 Control_rep3
==> sgRNA_Mapping_File-Fixed.tab <== sgrna Gene
Got this error
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgrna --gene_h dr=Gene --ctrl_sample_hdr=Sample --outprefix JACKS [2021-11-11 17:39:54,074] jacks: INFO Loading sample specification [2021-11-11 17:39:54,075] jacks: INFO Loading gene mappings [2021-11-11 17:39:54,078] jacks: INFO Loading data and pre-processing [2021-11-11 17:39:54,136] jacks: INFO Applying median normalisation [2021-11-11 17:39:54,184] jacks: INFO Collating 0 samples [2021-11-11 17:39:54,200] jacks: INFO Running JACKS inference /home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice return fun(*args, kwargs) /homes/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice. LOG.debug("After init, mean absolute error=%.3f,
=%.1f 2)0.5), w1.mean(), SP.median((w2-w12)0.5), x1.mean()w1.mean())) /home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, [2021-11-11 17:39:54,511] jacks: INFO Writing JACKS results /home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results] /home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results] (jacksenv) @.:$/JACKS>head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab=%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound)) /gpfs/fs1/home/mehrotras/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount) /home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice. LOG.debug("After W update, =%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean())) /home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice. LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x1 Changed to Match
head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab ==> Count_Matrix-Fixed.tab <== sgRNA Gene P23H_rep1 P23H_rep2 Control_rep1 Control_rep2 Control_rep3
==> sgRNA_Mapping_File-Fixed.tab <== sgRNA Gene
Error
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgRNA --gene_hdr=Gene --ctrl_sample_hdr=Sample --outprefix JACKS [2021-11-11 17:42:37,162] jacks: INFO Loading sample specification [2021-11-11 17:42:37,162] jacks: INFO Loading gene mappings [2021-11-11 17:42:37,164] jacks: INFO Loading data and pre-processing [2021-11-11 17:42:37,223] jacks: INFO Applying median normalisation [2021-11-11 17:42:37,272] jacks: INFO Collating 0 samples [2021-11-11 17:42:37,288] jacks: INFO Running JACKS inference /home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice return fun(*args, kwargs) /home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice. LOG.debug("After init, mean absolute error=%.3f,
=%.1f 2)0.5), w1.mean(), SP.median((w2-w12)*0.5), x1.mean()w1.mean())) /home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, [2021-11-11 17:42:37,602] jacks: INFO Writing JACKS results /home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results] /home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]=%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound)) /home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount) /home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice. LOG.debug("After W update, =%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean())) /home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice. LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x1 Here is Expsummary
cat Exp_Summary_JACKS.tab Replicate Sample P23H_rep1 P23H P23H_rep2 P23H Control_rep1 CTRL Control_rep2 CTRL Control_rep3 CTRL
These all are tab separated, I reconfirmed this.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/felicityallen/JACKS/issues/17#issuecomment-966680927, or unsubscribe https://github.com/notifications/unsubscribe-auth/AADIQIZWIGD2XQK7COVA6ILULRCD5ANCNFSM5HWQIMGA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
Hi Leo, I cannot say about the version, as there is none to show. I had done a recent pull ( last commit shown is Oct 2, 2020). There are different versions of examples to setup the experiment design, here and here, that i have tried to follow. I think you are right and that it could be the Exp design file is not set correctly. The issues is I am not sure which is right one? Based on your suggestion I made this change:
cat Exp_Summary_JACKS.tab
Replicate Sample CONTROL
P23H_rep1 P23H
P23H_rep2 P23H
Control_rep1 Control1 Control_rep1
Control_rep2 Control2 Control_rep2
Control_rep3 Control3 Control_rep3
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgRNA --gene_hdr=Gene --
rep_hdr=Replicate --sample_hdr=Sample --ctrl_sample_hdr=CONTROL --outprefix JACKS
I am getting
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgRNA --gene_hdr=Gene --
rep_hdr=Replicate --sample_hdr=Sample --ctrl_sample_hdr=CONTROL --outprefix JACKS
[2021-11-15 11:32:53,381] jacks: INFO Loading sample specification
[2021-11-15 11:32:53,382] jacks: INFO Loading gene mappings
[2021-11-15 11:32:53,384] jacks: INFO Loading data and pre-processing
[2021-11-15 11:32:53,443] jacks: INFO Applying median normalisation
[2021-11-15 11:32:53,468] jacks: WARNING Undefined variances in sample Control1, set --ctrl_genes input to JACKS to infer variances from control genes
[2021-11-15 11:32:53,471] jacks: WARNING Undefined variances in sample Control2, set --ctrl_genes input to JACKS to infer variances from control genes
[2021-11-15 11:32:53,473] jacks: WARNING Undefined variances in sample Control3, set --ctrl_genes input to JACKS to infer variances from control genes
[2021-11-15 11:32:53,478] jacks: INFO Collating 4 samples
Traceback (most recent call last):
...........
......
...
ValueError: 'Control_rep1' is not in list
So it seems that I need the third column. However, I am not sure how set this correctly. I have 3 WT/Controls and 2 muts/treatments.
Making this change
cat Exp_Summary_JACKS.tab
Replicate Sample CONTROL
P23H_rep1 P23H
P23H_rep2 P23H
Control_rep1 Control1 Control1
Control_rep2 Control2 Control2
Control_rep3 Control3 Control3
shows following error
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgRNA --gene_hdr=Gene --rep_hdr=Replicate --sample_hdr=Sample --ctrl_sample_hdr=CONTROL --outprefix JACKS
[2021-11-15 11:35:40,198] jacks: INFO Loading sample specification
[2021-11-15 11:35:40,199] jacks: INFO Loading gene mappings
[2021-11-15 11:35:40,201] jacks: INFO Loading data and pre-processing
[2021-11-15 11:35:40,259] jacks: INFO Applying median normalisation
[2021-11-15 11:35:40,294] jacks: INFO Collating 1 samples
Traceback (most recent call last):
...
.......
ValueError: None is not in list
Hello, I am trying to use JACKS and running into following issues:
Here are snippets of how various files look: head -n +4 Count_Matrix.tab
head Exp_Summary_JACKS.tab
head -n +3 sgRNA_Mapping_File.tab
Not exactly sure why any array slice will produce a mean of <0( assuming that is the error). The counts is tab separated and so are the other files as well. I do see a
Collating 0 samples
could this be the issue?Any help will be much appreciated.
Thanks, D