reduced_genome.sh gives no output

[Lissy28]

I am trying to run reduced_genome.sh on mm9 with dpnii digestion but it seems to freeze after producing the up.txt and down.txt files. When it did run to completion it deleted these files but left no reduced genome file

[rr1859]

Is there an *oligomatch.bed file?

[Lissy28]

I have fixed it now. The problem was I needed to use a genome.fa file from a different server location once I changes all the ${genome}.fas to the file location it worked.

Carol

On 20-07-2017 23:19, Ramya Raviram wrote:

Is there an *oligomatch.bed file?

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Links:

[1] https://github.com/rr1859/R.4Cker/issues/35#issuecomment-316846378 [2] https://github.com/notifications/unsubscribe-auth/Ac6tnj4mLg-sxUd32yKhikP99j1zVhpaks5sP9J_gaJpZM4OeSPs

-- Carol Edwards PhD, Department of Genetics University of Cambridge Genetics Building Downing Street Cambridge CB2 3EH Phone 44-1223-333981

[Lissy28]

Hi Ramya,

I have managed to get to the R stage but 2 of my libraries fail the QC as they are just under the 1 million reads threshold. Is there any way to change this threshold because I want to do the analysis on these libraries to confirm it is in agreement the the other analysis I have performed?

Many thanks

Carol

On 20-07-2017 23:19, Ramya Raviram wrote:

Is there an *oligomatch.bed file?

-- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub [1], or mute the thread [2].

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Links:

[1] https://github.com/rr1859/R.4Cker/issues/35#issuecomment-316846378 [2] https://github.com/notifications/unsubscribe-auth/Ac6tnj4mLg-sxUd32yKhikP99j1zVhpaks5sP9J_gaJpZM4OeSPs

-- Carol Edwards PhD, Department of Genetics University of Cambridge Genetics Building Downing Street Cambridge CB2 3EH Phone 44-1223-333981

[rr1859]

The QC is only printed as a warning - you can still continue with the pipeline. If they are just under 1 million then I would go ahead if they passed all the other criteria and if you are particularly interested in interactions that are in close linear scale to your bait.

[Lissy28]

Dear Ramya,

Thank you for your reply.

I have tried to continue with the analysis but running the near bait analysis fails on the 2 samples that have less than 1 million reads as they do not produce the lowinter.bed and highinter.bed files

this is the R input I used and error message.

my_obj = createR4CkerObjectFromFiles(files = c("Bl6_BC_Br1_Mat1_aligned_rm_self_und.bedGraph", "Bl6_BC_Br2_Mat2_aligned_rm_self_und.bedGraph", "Bl6_BC_Br3_Mat3_aligned_rm_self_und.bedGraph",

• "Bl6_CB_Br4_Pat4_aligned_rm_self_und.bedGraph", "Bl6_CB_Br5_Pat5_aligned_rm_self_und.bedGraph", "Bl6_CB_Br6_Pat6_aligned_rm_self_und.bedGraph"),
• bait_chr="chr12",
• bait_coord= 110779998,
• bait_name = "Gtl2",
• primary_enz = "GATC",
• samples = c("Mat1_Br1", "Mat2_Br2", "Mat3_Br3", "Pat4_Br4", "Pat5_Br5", "Pat6_Br6"),
• conditions = c("Mat_Br", "Pat_Br"),
• replicates = c(3,3),
• species = "mm",
• output_dir = "/Running_4Cker/Gtl2_Brain_results/",
• enz_file=enz_file) Bl6_CB_Br5_Pat5_aligned_rm_self_und.bedGraph has < than 1 million reads ( 945994 ). Does not pass QC. Bl6_CB_Br6_Pat6_aligned_rm_self_und.bedGraph has < than 1 million reads ( 830300 ). Does not pass QC. nb_results=nearBaitAnalysis(my_obj,k=5) [1] "Building adaptive windows..." [1] "Normalizing counts..." [1] "Generating synthetic samples...." [1] "Parameter estimation....." Error in if (as.character(windows[i, 1]) == chr & windows[i, 2] <= end & : missing value where TRUE/FALSE needed

Could you let me know if there is something I can alter when I run this.

Many Thanks for your time.

Carol Edwards

On 22-07-2017 01:54, Ramya Raviram wrote:

The QC is only printed as a warning - you can still continue with the pipeline. If they are just under 1 million then I would go ahead if they passed all the other criteria and if you are particularly interested in interactions that are in close linear scale to your bait.

-- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub [1], or mute the thread [2].

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Links:

[1] https://github.com/rr1859/R.4Cker/issues/35#issuecomment-317142682 [2] https://github.com/notifications/unsubscribe-auth/Ac6tnin4p3k6ixYXnD9JPR6MFzzJfD45ks5sQUhVgaJpZM4OeSPs

-- Carol Edwards PhD, Department of Genetics University of Cambridge Genetics Building Downing Street Cambridge CB2 3EH Phone 44-1223-333981

[Lissy28]

I have run into another issue with a second set of experiments. I have run the near bait analysis but when running the differential analysis I get this error.

Error in differentialAnalysis(obj = my_obj, norm_counts_avg = nb_results$norm_counts_avg, : could not find function "quartz"

On 22-07-2017 01:54, Ramya Raviram wrote:

The QC is only printed as a warning - you can still continue with the pipeline. If they are just under 1 million then I would go ahead if they passed all the other criteria and if you are particularly interested in interactions that are in close linear scale to your bait.

-- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub [1], or mute the thread [2].

*

Links:

[1] https://github.com/rr1859/R.4Cker/issues/35#issuecomment-317142682 [2] https://github.com/notifications/unsubscribe-auth/Ac6tnin4p3k6ixYXnD9JPR6MFzzJfD45ks5sQUhVgaJpZM4OeSPs

-- Carol Edwards PhD, Department of Genetics University of Cambridge Genetics Building Downing Street Cambridge CB2 3EH Phone 44-1223-333981

[rr1859]

Did you try a different value of k? Also how many reads does that the replicate that passed QC have? Im assuming you are running this on a windows machine - I apologize I did not account for that :) I have added a line to change it to windows(). If you don't mind can you re-install the package and test it? Thanks!

[Lissy28]

Hi, I re-installed the package and it all works now.

I have completed all my analysis using 4Cker and I was wondering if there is anyway to get the underlying values for the differential analysis. I have the bed file but this does not tell me how significant the difference is and in regions where both conditions are highly interacting which is the highest.

[rr1859]

Hi, I updated the script so that the output of DESeq2 is returned.

Ramya