User: SMK

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SMK1.8k
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Posts by SMK

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Comment: C: Perl Programming - How to join two columns of a text file, in which values of th
... 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 SMK1.8k
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Answer: A: Perl Programming - How to join two columns of a text file, in which values of th
... 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($a)` before you split it - In Perl, the ...
written 8 weeks ago by SMK1.8k
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Comment: C: First script trimmomatic
... Hi [https://www.biostars.org/u/56768/][1], I would suggest having a read of the book: "Bioinformatics Data Skills" by Vince Buffalo. At chapter 12: "Bioinformatics Shell Scripting, Writing Pipelines, and Parallelizing Tasks" you'll find very instructive information, especially in the section: "Proc ...
written 8 weeks ago by SMK1.8k
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Comment: C: How to calculate overlap of peptides between different categories to create Ven
... Cool, glad it helps! ...
written 8 weeks ago by SMK1.8k
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Comment: C: Finding all bases at a specific genomic position
... Can you try again by changing from `position, position+1` to `position-1, position` (in `bam.pileup`)? It should work as within pysam coordinates are 0-based. ...
written 9 weeks ago by SMK1.8k
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Comment: C: Finding all bases at a specific genomic position
... OK, it works in my case. Did you get any error, or just printing nothing? ...
written 9 weeks ago by SMK1.8k
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Answer: A: Finding all bases at a specific genomic position
... Hi [https://www.biostars.org/u/54815/][1], Try (updated): ``` vcf_reader = vcf.Reader(filename=input_vcf) for record in vcf_reader: position = record.POS for pileupColumn in bam.pileup("chr22", position-1, position, stepper='samtools', min_base_quality=0, ignore_overlaps=False, ignore_orph ...
written 9 weeks ago by SMK1.8k
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Answer: A: Rename fasta headers with file name + original header
... Hi [https://www.biostars.org/u/56613/][1], Try: ``` for fa in *.fasta; do fn=$(basename ${fa} .fasta) sed "s/^>/>${fn}_/" ${fa} > reID_${fa} done ``` [1]: https://www.biostars.org/u/56613/ ...
written 9 weeks ago by SMK1.8k
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Comment: C: How do I get ranges for first or last n nucleotides in genomicranges
... Can you show the problematic data as an example? :-( ...
written 9 weeks ago by SMK1.8k
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Comment: C: How do I get ranges for first or last n nucleotides in genomicranges
... 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 SMK1.8k

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