User: Carambakaracho
Carambakaracho • 2.2k
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Bioinformatics specialist at a medical device company
Posts by Carambakaracho
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... [bcftools][1]? Though this is probably not what you need.
Similar to sam/bam format, sometimes the meta information contains the software used for variant calling (see the source tag, for example).
However, the tag is optional, not clearly specified and in most interpretations you get the softwar ...
written 5 weeks ago by
Carambakaracho • 2.2k
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... There's four assemblies at the NCBI:
https://www.ncbi.nlm.nih.gov/genome/browse/#!/eukaryotes/145/
In case your genes of interest are not annotated, but you know their sequence, why don't you blast them against your genome? ...
written 6 weeks ago by
Carambakaracho • 2.2k
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... bloody ****, I should pay attention to details...
Well, technically at least, DESeq2. EdgeR, and limma/voom are R . For what it's worth anyway ...
written 8 weeks ago by
Carambakaracho • 2.2k
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... I'm not the best source, as I'm behind on most of the active research, but I remember the feeling. For beginners it's not so easy to separate the wheat from the chaff, imo this would be your teacher's responsibility, though.
Let me give it shot: for data analysis milestones comparable with what yo ...
written 8 weeks ago by
Carambakaracho • 2.2k
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... I admit, had you asked me the questions above at the level of the OP with the breadth of bioinformatics today, I was overwhelmed, too and I started when [Koonin's COGs][1] where bleeding edge...
[1]: https://pubmed.ncbi.nlm.nih.gov/10592175/ ...
written 8 weeks ago by
Carambakaracho • 2.2k
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... One of a set of PCR duplicates? Can you filter them out with picard tools? What does the bam flag say? Did you try a different aligner, e.g. BWA mem? ...
written 8 weeks ago by
Carambakaracho • 2.2k
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... [@Santosh][1], thank you. This certainly among the best answers I've read on Biostars.
I'd like to add a tiny extension for transposition of tibbles [originally from stackoverflow][2], assuming genenames being the name of the first column:
dt <- d %>%
gather(var, val, 2:ncol(d)) ...
written 9 weeks ago by
Carambakaracho • 2.2k
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Comment:
C: Bash script problem
... Just to make sure you're not hunting a ghost: the sorted bam in `s$1` contains all reads?
I don't see any obvious show stopper, so maybe your input interferes with the call. You might want to try [parameter substitution][1]
bedtools intersect -wa -a s${1} -b ${2} > KRAS_s${1}
[1]: https ...
written 10 weeks ago by
Carambakaracho • 2.2k
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Comment:
C: Bash script problem
... Hi Steven, there's some additional info needed to support you:
Is this the full body for the script? How do you run the bash script? Can you `echo $1` and `echo $2`? Does this yield what you expect?
I don't think `>` should be the problem... ...
written 10 weeks ago by
Carambakaracho • 2.2k
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... When you use `-Y` on secondary alignments the sequence that aligned to the primary alignment won't get hard clipped but softclipped, in my case I exploited that for split reads when a rearrangement occurred in the middle of the read. This means the clipped sequence will be preserved in the bam line ...
written 10 weeks ago by
Carambakaracho • 2.2k
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