User: cmdcolin

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cmdcolin1.1k
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Posts by cmdcolin

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Comment: C: Bio-DB-HTS installation and ensembl-vep
... Have you tried simply installing it using "cpan Bio::DB::HTS"? ...
written 19 days ago by cmdcolin1.1k
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Comment: C: Getting these files from different parts of genome
... I don't know a lot about this software but appears to take "regions of interest" rather than whole genome information about this data https://github.com/reimandlab/ActiveDriverWGS I would recommend probably using the UCSC table browser to get BED output for this info also ...
written 26 days ago by cmdcolin1.1k
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Comment: C: IGB won't open .gff file.
... The GFF contains the annotation. It can sometimes contain the "genome sequence" using embedded FASTA that Juke-34 refers to, but more often the genome sequence is in a FASTA file (extension .fa, .fasta, or .fna sometimes from NCBI). You can download the FASTA from NCBI too and probably will open tha ...
written 27 days ago by cmdcolin1.1k
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Answer: A: Plotting MBD-seq results
... The `deepTools` package can do things like this https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html You would prepare coverage files in the form of bigwigs with `computeMatrix` https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html\ Converting aligned ...
written 4 weeks ago by cmdcolin1.1k
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Comment: C: Parse sim4 output alignment format
... I was going to suggest using BioPerl sim4 SearchIO parser but this is not appear to be working for me...the parsed resuts in something like this appear wrong to me.... `$searchio = Bio::SearchIO->new(-file => 'test.blastx', -format => 'sim4'); ` ...
written 4 weeks ago by cmdcolin1.1k
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Answer: A: Extract reads within given region, and their mates
... The tool "Bazam" is built for this purpose but it outputs the reads in fastq https://github.com/ssadedin/bazam Ref https://www.biorxiv.org/content/10.1101/433003v2 ...
written 5 weeks ago by cmdcolin1.1k
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Comment: C: Efficent Estimation of Sequencing Coverage
... You can use samtools idxstats to get number of reads that are aligned to any given chromosome, which would be essentially be what you are looking for (don't need any percentage as this gives you the number of reads actually aligned). Sum over all chromosomes (exclude the * line which are unmapped re ...
written 5 weeks ago by cmdcolin1.1k
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Comment: C: How remove stop codons from gff file?
... you are asking essentially a duplicate question of https://www.biostars.org/p/362294/#362436 ...
written 5 weeks ago by cmdcolin1.1k
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Comment: C: Extract read sequence from BAM files depending on the alignment coordinates
... I think this is not true. It will output reads overlapping the given region. The samtools documentation http://www.htslib.org/doc/samtools.html says "You may specify one or more space-separated region specifications after the input filename to restrict output to only those alignments which **overlap ...
written 6 weeks ago by cmdcolin1.1k
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Comment: C: Extract read sequence from BAM files depending on the alignment coordinates
... It will output all reads overlapping the region, quick sanity check verifies that some reads with start coordinate less than my query do show up ...
written 6 weeks ago by cmdcolin1.1k

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