User: Vivek
Vivek • 1.7k
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Bioinformatics Developer
Posts by Vivek
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... I'd assume ref.core.targets_merged.bed is a subset of ref_plus_utr.targets.bed. If so that is the file you should use, if not merge the files together using BEDtools merge and use the resulting bed file. You can ignore the baits bed files. ...
written 2 days ago by
Vivek • 1.7k
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... You can align the sequences using BLAT.
https://genome.ucsc.edu/cgi-bin/hgBlat?command=start
Convert the top alignments from the resulting PSL file to BED format and use BEDtools to check the intersection with your coordinates. ...
written 10 days ago by
Vivek • 1.7k
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... You cannot assume that, some exome capture designs also cover UTR regions. You need to ideally get a specific bed file of targeted regions or alteast the name of the capture kit used so you can go to their webpage and download target regions from there. ...
written 25 days ago by
Vivek • 1.7k
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... So did you check if the zero coverage positions lie within your targeted regions? If they don't, you can safely exclude them, if they do lie in your target regions and there is a large chunk of them you can ask your sequencing provider about the poor quality. ...
written 25 days ago by
Vivek • 1.7k
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... If this is exome sequencing data, you should see zero depth in off target regions after QC to remove mis-mapped reads. Did you try restricting your query to a BED file of target regions? ...
written 25 days ago by
Vivek • 1.7k
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... I'm not sure what you mean by all BAM files, in general its best to view coverage over a single sample (BAM) rather than combine across samples as you'd otherwise miss the variation between samples. You should be able to plot all chromosomes at once even if its a WGS experiment but if it is too cumb ...
written 4 weeks ago by
Vivek • 1.7k
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... samtools mpileup your.bam | awk '{print $1"\t"$2"\t"$4}'
Gives you coverage at each chr:pos
There after you can use something like ggplot in R to plot a histogram of coverage. ...
written 4 weeks ago by
Vivek • 1.7k
0
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125
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Comment:
C: tips for checking variants in IGV
... Defaults should be fine, I never experimented with those. You'll be doing manual inspection anyways. ...
written 8 weeks ago by
Vivek • 1.7k
2
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... Some things I look at:
1. Base qualities at the locus and mapping qualities of the reads supporting the variant
2. Frequency of mutations or INDELs within 1 KB region on either side
3. Allele fraction on both strands ...
written 8 weeks ago by
Vivek • 1.7k
3
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... PIs usually don't consider hiring someone as a Bioinformatician with no prior experience or relevant education, its a high pressure job around deadlines where the learning curve is pretty steep even for well trained people.
However some larger genome centers have entry level QC positions available ...
written 8 weeks ago by
Vivek • 1.7k
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