User: SMK
SMK • 1.8k
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Posts by SMK
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... I've updated some points and suggestions for you. Have fun with Perl, but do take the suggestions from [https://www.biostars.org/u/24526/][1] into consideration... ;-)
[1]: https://www.biostars.org/u/24526/ ...
written 8 weeks ago by
SMK • 1.8k
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... Hi [https://www.biostars.org/u/56775/][1],
Some points:
- Try always including `use strict;` and `use warnings;`
- You have to add `OUT` after `print` to really write things to `Alu_subfamlength3`
- If column 10 is the last column, you have to do `chomp($a)` before you split it
- In Perl, the ...
written 8 weeks ago by
SMK • 1.8k
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Comment:
C: First script trimmomatic
... Hi [https://www.biostars.org/u/56768/][1],
I would suggest having a read of the book: "Bioinformatics Data Skills" by Vince Buffalo. At chapter 12: "Bioinformatics Shell Scripting, Writing Pipelines, and Parallelizing Tasks" you'll find very instructive information, especially in the section: "Proc ...
written 8 weeks ago by
SMK • 1.8k
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... Cool, glad it helps! ...
written 8 weeks ago by
SMK • 1.8k
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... Can you try again by changing from `position, position+1` to `position-1, position` (in `bam.pileup`)?
It should work as within pysam coordinates are 0-based. ...
written 9 weeks ago by
SMK • 1.8k
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... OK, it works in my case. Did you get any error, or just printing nothing? ...
written 9 weeks ago by
SMK • 1.8k
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... Hi [https://www.biostars.org/u/54815/][1],
Try (updated):
```
vcf_reader = vcf.Reader(filename=input_vcf)
for record in vcf_reader:
position = record.POS
for pileupColumn in bam.pileup("chr22", position-1, position, stepper='samtools', min_base_quality=0, ignore_overlaps=False, ignore_orph ...
written 9 weeks ago by
SMK • 1.8k
2
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... Hi [https://www.biostars.org/u/56613/][1],
Try:
```
for fa in *.fasta; do
fn=$(basename ${fa} .fasta)
sed "s/^>/>${fn}_/" ${fa} > reID_${fa}
done
```
[1]: https://www.biostars.org/u/56613/ ...
written 9 weeks ago by
SMK • 1.8k
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... Can you show the problematic data as an example? :-( ...
written 9 weeks ago by
SMK • 1.8k
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... Alright, `flank` + `range`. ;-)
```
> flank(range(grTarget), width = -21, start = TRUE)
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
[1] chr12 25398324-25398344 *
-------
seqinfo: 1 sequence from an unspecified gen ...
written 9 weeks ago by
SMK • 1.8k
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