Moderator: finswimmer
finswimmer ♦ 4.5k
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Posts by finswimmer
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... An `awk` solution:
$ awk '$0 ~ "^>" {match($1, /^>([^_]+)_/, id); filename=id[1]} {print >> filename}' seqs.fna
fin swimmer ...
written 13 hours ago by
finswimmer ♦ 4.5k
0
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141
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Comment:
C: Google search for gene variants
... What's your question/intention of this post? ...
written 15 hours ago by
finswimmer ♦ 4.5k
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... I guess this more a limitation by the OS.
On many linux distribution the maximum number of open files is 1024. You can find it out on your system with
$ ulimit -n
There seems to be many ways to increase the number if necessary, e.g. like [here][1]
fin swimmer
[1]: https://easyengine.io/t ...
written 15 hours ago by
finswimmer ♦ 4.5k
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... > Yes, because if you don't trim the adapters, the reads won't merge
> anyway.
AFAIK `bbmerge` can use the adapter information for merging. So don't trimming before merging increases the merging rate.
fin swimmer
...
written 23 hours ago by
finswimmer ♦ 4.5k
6
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1
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115
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... Use [bedtools][1]:
$ bedtools intersect -a input.vcf -b genes.gff -header -wa > output.vcf
---
**EDIT:**
For (very) large `vcf` files it might be more efficient to `bgzip` and `tabix` index the `vcf` file, convert your `gff` to `bed` and use `tabix` to query the regions
**1. bgzip and ind ...
written 1 day ago by
finswimmer ♦ 4.5k
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Comment:
C: Alignment with BWA and SAMtools
... Hello Shello,
now we are back to the questions I asked at the very [beginning][1]. And: What kind of sample is it?
[1]: https://www.biostars.org/p/332056/#332080 ...
written 2 days ago by
finswimmer ♦ 4.5k
1
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4
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304
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4
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... What about this (based on your header description [here][1])?
$ cut -f1 -d "-" *.fa|awk -v RS=">" -v FS="\n" -v OFS="\n" '{for(i=2; i<=NF; i++) {seq[$1] = seq[$1]$i}}; END {for(id in seq){print ">"id, seq[id]}}' > combined.fa
[1]: https://www.biostars.org/p/332853/#333193 ...
written 4 days ago by
finswimmer ♦ 4.5k
0
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1
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154
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... Hello pd3,
thank you for your response. Unfortunately this isn't an answer to my initial question about the differences between `|` and `||`.
As I [wrote][1] a little bit later the difference between `&` and `&&` is clearly explained in the manual, even if the description "&& ( ...
written 5 days ago by
finswimmer ♦ 4.5k
2
votes
1
answer
78
views
1
answers
... Use [seqkit][1]:
$ seqkit rmdup input.fa > output.fa
[1]: https://bioinf.shenwei.me/seqkit/usage/#rmdup ...
written 5 days ago by
finswimmer ♦ 4.5k
0
votes
4
answers
304
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4
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... Could you please explain how the bacterias are delimited from the genes? ...
written 6 days ago by
finswimmer ♦ 4.5k
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