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@wdduncan @lwaldron @lgeistlinger @cmungall
From our conversation on Thursday (thank you btw @wdduncan, it was really helpful), we discussed how to structure the relationship between the microbiome…
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Hi Developer!
I've been working with the pipeline described in the Nature Protocols paper (2016). I've done everything up to the ballgown step. Instead of using ballgown, I've used prepDE.py to get…
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We're interested in quantifying isoform specific stability with a custom set of 3'UTRs
If we were to tweak the bam2bakR pipeline, supplementing a custom set of isoforms as separate ‘genes’ to a sta…
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Hey everyone, I am testing your tool to check for contamination on my scRNAseq+CITEseq experiment. I have one issue and some questions:
1. When running the pipeline on all the features and antibody, …
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I installed using mamba. When I run, I get the following error concerning module 'skip'. I checked and it's installed and Python finds it just fine. Any idea as to what to try?
[2022-09-29 14:16 IN…
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Hello,
I identified A and B compartments in my data at three resolutions (10Kb, 100Kb and 1Mb):
'''
fanc compartments -g $CHROMS_PATH -d $DOMAIN_OUTPUT $FILE -x $CHROMS2EXCLUDE
'''
I am a b…
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Hi, I have been using STAR for a while now but still cannot find the right settings that give a satisfactory mapping speed and efficient mapping.
I have short RNA sequencing reads (sRNAs, 22-24nt) t…
brobr updated
4 years ago
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Whole-genome sequencing of S. paradoxus mutation accumulation lines
DNA extracted using Zymo YeaSTAR Genomic DNA kit
Libraries prepped using homemade protocol (no kit, can find out more info if ne…
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Hi Kieran,
Did you assess the performance of the new version of the package versus the previous one? I have noticed some things:
- it seems to be rather sensitive to the `initial_shrinks` parame…
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This issue covers 3 different types of CRISPR screens.
Related publications:
* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8443183/
* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181115/
* htt…