User: Fedster

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Fedster30
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Posts by Fedster

<prev • 21 results • page 1 of 3 • next >
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Comment: C: bowtie2 and FLASh
... I asked Julian Catchen (who wrote Stacks) and he recommends NOT using it. ...
written 5 months ago by Fedster30
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bowtie2 and FLASh
... I was wondering whether there is a proper way of using bowtie2 after going through my reads with FLASh (https://ccb.jhu.edu/software/FLASH/). Flash would produce 3 files: - extended fragments - non extended R1 fragments - non extended R2 fragments I could call bowtie2 twice (one for the ext ...
bowtie2 written 5 months ago by Fedster30
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Comment: C: samtools: splitting a bam file putting all scaffolds together
... works, if you add it as an answer I will accept it as the correct one. Cheers ...
written 8 months ago by Fedster30
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Comment: C: samtools: splitting a bam file putting all scaffolds together
... basically `samtools view my.bam contig* -b -o output.bam` does not work ...
written 8 months ago by Fedster30
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Comment: C: samtools: splitting a bam file putting all scaffolds together
... I do not want to run all chroms and contigs in parallel, I want to get all the fragments mapping to any contig (not in a chromosome) out in one single step and dump in one single file. My problem is not listing all possible fragments/contigs/chroms, it using a wildcard in samtools view to get out s ...
written 8 months ago by Fedster30
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samtools: splitting a bam file putting all scaffolds together
... I have some bam files that I want to split. The reference genome has 22 chromosomes and a bunch of unplaced scaffolds. I can easily split the bam files chromosome by chromososme samtools view my.bam chromsosmeI -b -o my_chromosomeI.bam I can do the same *scaffold by scaffold*, but I would li ...
splitting bam samtools scaffold written 8 months ago by Fedster30 • updated 8 months ago by finswimmer12k
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Comment: C: Freebayes outputs only one individual out of many
... and samtools view S-177.sorted.bam |head -n5 K00335:147:HL3KJBBXX:7:1227:25286:38627 0 MT 6894 1 64M * 0 0 CTGCTAAACGTGAAGTTTTAGCAGTTGAAATAACAACAACAAACGTCGAGTGACTTCACGGCTG JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ>JJJ AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0XG:i:0 NM:i:0 MD: ...
written 9 months ago by Fedster30
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Comment: C: Freebayes outputs only one individual out of many
... technically I used not just x.bam but w whole lot of bams (sorted) generated by bowtie2. Using a real sample name: samtools view -H S-177.sorted.bam |head @HD VN:1.0 SO:coordinate @SQ SN:MT LN:15742 @SQ SN:groupI LN:28185914 @SQ SN:groupII LN:23295652 @SQ SN:groupIII LN:167 ...
written 9 months ago by Fedster30
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Comment: A: Freebayes outputs only one individual out of many
... Ok, I tried to add RG tags and it is just basically a fail. I can add tags, but freebayes still does not like them. Given a file for ID x samtools addreplacerg -r ID:x -r SM:x -o x.bam x.sorted.bam adds a tag (at least, I can see a tag in the file and I get no error), but to no avail: ...
written 9 months ago by Fedster30
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Comment: C: Freebayes outputs only one individual out of many
... One thing that is not clear from bamaddrg is whether the option -L (list of files) is then needed. Is it? ...
written 9 months ago by Fedster30

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