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Recent Replies
Comment: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
by
gynecoloji
•
0
Thanks for your response.
I think it may be better to keep those repetitive regions and only filter out the blacklisted regions.
This is a …
Comment: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
by
jared.andrews07
★
18k
IDR addresses a different problem than removal of reads aligning to blacklist reads, though it's unquestionably useful for deriving more ro…
Comment: Issue with Package installation in R.
by
GenoMax
151k
Simply posting a snippet of error message in a question is the reason you have not received any responses.
Please make an effort to formu…
Answer: Building database with snpEff -- -gtf22 option not recognized/file not read
by
michael.dhar
•
0
Based on the ordering of the commands here: https://github.com/pcingola/SnpEff/issues/583
I believe I just needed to place the "build" c…
Comment: WGCNA blockwiseModules function for small datasets
by
ATS
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That's great to know. Thanks for your input!
Answer: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
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LChart
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It should be noted that concerns about mapping artifacts in ChIP-seq really come from an era where reads were 36bp (or even 25bp!) in lengt…
Comment: WGCNA pickSoftThreshold problem
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LChart
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AGain you seem to be over-filtering. Your mean.k and median.k are really low, so I think the number of input genes you used for this is ver…
Answer: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
by
jared.andrews07
★
18k
I am going to guess you've seen/thoroughly read [this paper about the ENCODE blacklist regions](https://www.nature.com/articles/s41598-019-…
Comment: Using VEP custom input
by
Sd
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Initially, I converted the file to GFF3 format in order to run VEP, but I got warnings and couldn’t figure out what the problem was.
GFF…
Comment: nanopore unaligned bam files
by
colindaven
7.6k
When you have a bam make sure you check the methyl tags MM and ML are present. Something like
samtools view -h x.bam | grep MM
sam…
Comment: nanopore unaligned bam files
by
sarahmanderni
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130
yes keeping both mapping info and methylation info at the same time is the intention. Thanks so much for the reosponse! I will try it
Comment: nanopore unaligned bam files
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GenoMax
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> OP wants to align AND keep the methylation info
Then use something like
minimap2 -t use_N_cores -Y -y -ax map-ont your_minimap_ind…
Comment: nanopore unaligned bam files
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lieven.sterck
15k
I think OP wants to align AND keep the methylation info, which is indeed the tricky part ...
Not entirely sure but I think the `dorado ali…
Answer: nanopore unaligned bam files
by
GenoMax
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> is this normal to receive the bam files in this shape and
Yes. If you asked for methylation calls then this is a way to capture that i…
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ATpoint
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How were these tracks generated? Is it bigwig files (or bedGraphs) at single-base resolution or was it like deeptools bamCoverage which by …
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