Moderator: swbarnes2
swbarnes2 ♦ 3.5k
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Posts by swbarnes2
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... I think in general, identifying the genes responsible is not going to be of any biological significance. ...
written 5 days ago by
swbarnes2 ♦ 3.5k
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... If the gene runs backwards, exon 1 should have the highest genomic position. But regardless of the direction of the gene, exon #1 is first of its transcript (it might not be first in another transcript of the same gene). If you are pulling it out by name or exon ID, it should be in the "right" ori ...
written 5 days ago by
swbarnes2 ♦ 3.5k
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... Exon rank is the # that the exon is in that transcript. First exon is rank 1, second is rank 2, etc.
"+" and "-" tell you of the transcript runs forward or reverse on the genome. If you are getting your sequence from the genome coordinates, you might need to rev comp it to get the sequence in the ...
written 5 days ago by
swbarnes2 ♦ 3.5k
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... You should be able to do this with a little grep. Something like
samtools view sort.bam | cut -f 1,10 | grep 'AAAAAAA$' ...
written 10 days ago by
swbarnes2 ♦ 3.5k
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... Just checking wikipedia, which isn't necessarily quoting the true authority, the + line has to either be blank, or a copy of the @ line.
So I'd fix that, or fix the perl script to not mind that, and try again. ...
written 11 days ago by
swbarnes2 ♦ 3.5k
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... What software is making vcfs with those tags? ...
written 11 days ago by
swbarnes2 ♦ 3.5k
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... Are you sure you have enough depth do to variant calling? ...
written 12 days ago by
swbarnes2 ♦ 3.5k
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Comment:
C: Non-coding RNA detection
... Are you sure that all kinds of non-coding RNA will be caught by the library prep technique used? ...
written 13 days ago by
swbarnes2 ♦ 3.5k
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... Notice the number mapped is nearly the same. Samtools flagsat is just reading the flags in the sam file, I don't know that either bwa program will assign a QC fail flag to the resulting sam file.
As a sanity check, how many reads does the fastq really have? 1.6 billion reads is just about an en ...
written 14 days ago by
swbarnes2 ♦ 3.5k
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Answer:
A: STAR options for RNA Seq
... Of those last three options, I never have used the introny ones (but my lab cares more about counting than analyzing splice sites), and I always include unmapped reads in the .bam. It's just so much easier down the road if you or someone else wants to reanalyze data to know that you didn't wrongly ...
written 17 days ago by
swbarnes2 ♦ 3.5k
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