Moderator: swbarnes2
swbarnes2 ♦ 5.0k
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Posts by swbarnes2
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... What are the three most common sources of programming errors? Poor naming, and 1-off errors. ...
written 11 hours ago by
swbarnes2 ♦ 5.0k
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... I think your tutorial is very old. Add "version=75" to your useMart command, and you'll see gene coordinates close to the tutorials. ...
written 16 hours ago by
swbarnes2 ♦ 5.0k
3
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Answer:
C: StringTie missing header
... Umm, where in that command line are you telling StringTie where your bam is? ...
written 2 days ago by
swbarnes2 ♦ 5.0k
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... You can just cat fastq.gz files together.
cat bacteria1*.fastq.gz > large_bacteria1.fastq.gz
for example. ...
written 2 days ago by
swbarnes2 ♦ 5.0k
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... I noticed that before, but not with RNAseq. It was a kind of artificial set up, where the sequence of interest was exactly 42 bases long, and so we sequenced for just 43 bases (so that there would be 42 bases with post-phasing data). And I noticed that a lot of reads had the last letter trimmed, b ...
written 3 days ago by
swbarnes2 ♦ 5.0k
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Comment:
C: UMI Tools Dedup
... And the conclusion of the link seemed to be that for the most part, that's just how the software is. It has to remember all the reads and their indices that it comes across; this is going to be memory intense. ...
written 7 days ago by
swbarnes2 ♦ 5.0k
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158
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... I don't think STAR can take them both together. I'd process the two separately, and merge results at the end if it looks like the two experiments are telling you the same thing. ...
written 8 days ago by
swbarnes2 ♦ 5.0k
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... A fastq or bam is not chromosome-specific unless someone aligns it and picks out the reads aligning to one chromosome. So you generally won't be looping through multiple files for a single sample. You'll just align one sample's fastq to the whole genome, and have one bam for the whole genome.
...
written 8 days ago by
swbarnes2 ♦ 5.0k
1
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97
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Answer:
A: Problem with STAR aligner
... A few points:
STAR's genomic alignment is very good about making an alignment work, even if the ends of the read don't match. (the alignment to transcriptome that it can produce is however very strict about throwing away reads that require clipping to align)
The lab running the libraries is spendi ...
written 10 days ago by
swbarnes2 ♦ 5.0k
0
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177
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Comment:
C: DESeq2 and integers values
... Or, use `--fraction`, but round your counts before giving them to DESeq. ...
written 14 days ago by
swbarnes2 ♦ 5.0k
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For C: how to identify a sequencing sample's gender
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3 months ago,
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For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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7 months ago,
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For A: Blast: Homology Or Similarity?
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For C: how to identify a sequencing sample's gender
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For A: Is It Safe To Remove Exact Duplicate Reads In The Denovo Transcriptome Assembly?
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10 months ago,
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For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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