User: shimbalama

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shimbalama10
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Posts by shimbalama

<prev • 5 results • page 1 of 1 • next >
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Comment: C: How to extract reads with no INDEL?
... Hi all. Any way to modify this so it finds read with deletions > 20bp? samtools view -h in.bam chr1:12340-200000 \ | awk '$1 ~ "^@" || $6 ! "20D"' \ | samtools view -b - > out.bam Would give reads with exactly 20 bp, right? Is it possible to do > 20bp? ...
written 5 days ago by shimbalama10
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Comment: C: Extract gene IDS from GFF3 based on coordinates from another file
... you just need a little python. ie, if range start < annotation start < range end. and same for annotation end. or just make a range and ask if it's in that range... if u are going to have to do this sort of thing regularly u need to learn py. ...
written 4 months ago by shimbalama10
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Answer: A: Difference between genome assembly and genome sequence alignment to a reference
... HI, Your question is a little unclear but I think I understand. You're talking about assembly Vs mapping for SV detection, right? To be clear, you can't do genome sequence alignments, except maybe for something as small as a virus like COIVD19. I was further confused, as a third option exists - to ...
written 5 months ago by shimbalama10
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Answer: A: Split multi-fasta file into smaller files using R
... hi. what you want to do is very easy with python and biopython. if ur supervisor said to use a for loop in R then they clearly aren't a Bioinformatician - avoid iterating in R. I'm using one hand on a phone so this wont be syntacticly correct but it should get u close. there are faster ways, like ...
written 6 months ago by shimbalama10
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IGB normalisation of reads
... Hi there, I've been tasked with visualising some RNAseq data (bacterial). I've been instructed to use IGB over IGV (which I'm more familiar with) as it can normalise the read counts so they are comparable. I've got my reference loaded with bams but I can't see any mention of a normalisation tool in ...
rnaseq next-gen igb normalisation rna-seq written 3.9 years ago by shimbalama10 • updated 3.9 years ago by Mason Meyer110

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Popular Question 3.6 years ago, created a question with more than 1,000 views. For IGB normalisation of reads

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