User: phosphodiester_bond

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Posts by phosphodiester_bond

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Comment: C: What is the best pipeline step to merge replicates?
... Thank you, I see now how this is probably not something with a generalizable solution (which is why I kept my original post intentionally vague). ...
written 5 weeks ago by phosphodiester_bond0
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Comment: C: What is the best pipeline step to merge replicates?
... Sorry about the extreme vagueness, I just edited my original post. This is ATAC-seq data that I'm pulling from GEO accessions, all uploaded by other labs. Most of these are biological replicates. ...
written 5 weeks ago by phosphodiester_bond0
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What is the best pipeline step to merge replicates?
... Based on your experience, at which point would you recommend merging the reads from multiple ATAC-seq replicates (biological replicates, for the most part)? And most importantly, why? I saw at Encode they first process the samples independently up to the BAM files, and merge all BAM files using sa ...
pipeline sequencing written 5 weeks ago by phosphodiester_bond0 • updated 5 weeks ago by Friederike1.8k
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Answer: A: What are the best tools for differential detection between ATAC-seq samples?
... Once you have your peaks for each condition, you can try DAStk, a tool recently put out for that purpose: https://biof-git.colorado.edu/dowelllab/DAStk ...
written 6 weeks ago by phosphodiester_bond0
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Answer: A: Differential Peak Expression in ATAC-seq data
... You can try DAStk, a tool recently put out for that purpose: https://biof-git.colorado.edu/dowelllab/DAStk ...
written 6 weeks ago by phosphodiester_bond0
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Comment: C: How To Get The Sequence Of A Genomic Region From Ucsc?
... Thanks, this is really handy!! ...
written 9 months ago by phosphodiester_bond0
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Comment: C: liftOver narrowPeak file
... Just curious if you've ever figured this out. I'm wondering the same for GRCh38-mapped narrowPeak files to hg19. I suspect getting rid of the offending columns is not advisable. ...
written 12 months ago by phosphodiester_bond0
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Answer: A: error in macs2 usage
... BTW, looks like a bug but I'm waiting on the author to confirm. I didn't see where that variable is used anywhere else, so I just changed that line cited in the error message to hardcode the temp directory in my cluster: `tempfile.tempdir = '/tmp/'` Maybe this was intended to have a `--tempdir` ar ...
written 14 months ago by phosphodiester_bond0
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Answer: A: error in macs2 usage
... Have you figured this one out, Sara? I'm running into the exact same issue (using build 2.1.1.20160309). My command looks like: macs2 callpeak --nomodel --format SAM -t /path/to/somefile.sam --shift -100 --extsize 200 -B --broad --outdir /the/output/dir/ I've also tried without `--outdir`, but ...
written 14 months ago by phosphodiester_bond0
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Comment: C: What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
... I'm also suspicious of these instructions in their pipeline since the "--strata" and "-k 1" options are incompatible. Not sure if we should ditch "--strata" or use a higher value for "-k" in case of overlaps. What do *you* guys normally use to align ATAC-Seq data? ...
written 17 months ago by phosphodiester_bond0

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