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Comment: Understanding STAR output (Aligned.out.sam file)
by
GenoMax
142k
Refer to SAM alignment format: https://samtools.github.io/hts-specs/SAMv1.pdf
Check section 1.4.
Answer: Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genom
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LChart
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Step 1: Go to TCGA in the GDC and open the Cohort Builder
https://portal.gdc.cancer.gov/analysis_page?app=CohortBuilder&tab=general
Step …
Comment: Where to get the following bed file?
by
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142k
SeqCap kits are discontinued. If you don't find the said file your will need to email Roche Support per this page: https://sequencing.roche…
Answer: Where to get the following bed file?
by
LChart
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UCSC maintains a list of exome probe sets and targets. You could check there:
https://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/
Comment: How to compute TPM normalized values for TCGA miRNA data?
by
Ngrin
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0
Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
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390
It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
Comment: Problem with Seurat package in PercentageFeatureSet function
by
bk11
★
2.4k
Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
Answer: How to compute TPM normalized values for TCGA miRNA data?
by
dsull
★
6.0k
TPM is irrelevant for miRNA-seq; CPM works fine.
TPM tries to adjust for length effects by dividing by gene length (e.g. reducing the im…
Comment: Applying the metacell2 algorithm using python
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Wayne
★
2.0k
"I'm also unsure what qualifies as a lateral gene."
The [README where you reference](https://metacells.readthedocs.io/en/latest/readme.htm…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
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Ah, yes this makes sense! I knew this was an issue with, say, using kraken2 on shotgun metagenomic reads, but I don't have a lot of experi…
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Qroid
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Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
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390
If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
Comment: anRichment is missing
by
GenoMax
142k
Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.
Comment: anRichment is missing
by
Tatyana
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0
Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(
Comment: anRichment is missing
by
GenoMax
142k
See this link for the WGCNA documentation and code from Peter Langfelder : https://bioinformatics.stackexchange.com/questions/21885/where-t…
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