User: Cookie-san

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Cookie-san40
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1 year, 9 months ago
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Posts by Cookie-san

<prev • 27 results • page 1 of 3 • next >
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Comment: C: getting sequence by combining reference and variants (fasta and vcf files)
... Also, as of July 2019, ```FastaAlternateReferenceMaker``` skips heterozygous ALT allelic sites. ...
written 9 weeks ago by Cookie-san40
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Comment: C: Emboss seqret - problem conversion gff+fasta to EMBL
... Thank you for the tool! ...
written 11 weeks ago by Cookie-san40
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Comment: C: Hard time trying to calculate Allele Frequency and DP from Platypus
... This is amazing, thank you :D ...
written 12 weeks ago by Cookie-san40
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Comment: C: Bioinformatics Project this summer
... You can work remotely. You can contact a mentor by video chat and meet them once a week/two weeks or whatever. Do you have the recommended hardware and software for whatever project you want to work under? NGS data analysis requires a lot of computational power, but this again depends on whatever o ...
written 3 months ago by Cookie-san40
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Answer: A: Coverage of exome
... You can use QualiMap :D ...
written 3 months ago by Cookie-san40
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NOISeq Fold Change calculation seems off?
... I tried doing DGE analysis using NOISeq with no replicates. I got the final results as Control_mean Treated_mean M D prob ranking Length GC Chrom GeneStart GeneEnd Biotype ENSG00000000003 1726 1696 0.02529629 30 0.2973327 30.000011 2206 40.40 X 100627109 100639991 protein_coding ENSG0 ...
rna-seq written 3 months ago by Cookie-san40
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Comment: C: Problem in running NOISeq-sim
... Hey, can you give the output of SampleInfo? Maybe there's an issue with that. ...
written 3 months ago by Cookie-san40
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Answer: A: Variant call format (VCF) file, how to get statistics per sample?
... Hi! You can try bcftools stats. Also vcflib's vcfstats. bcftools stats can also do comparisons and gives a much more detailed output that vcflib vcfstats. Edit: ALSO. If you try and use both vcfstats and bcftools stats, your stats won't be quite the same. I'm trying to figure out how the code diff ...
written 3 months ago by Cookie-san40
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Comment: C: bcftools mpileup --max depth : What would be a reasonable setting for this optio
... Thank you for your reply. I had to run the command urgently and set the parameter to 8000 - the samtools mpileup default. ...
written 3 months ago by Cookie-san40
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Comment: C: how is the output of bcftools stats calculated?
... To anyone looking for the answer to these questions, its here: https://github.com/samtools/bcftools/issues/316 The poster actually posted the same question on the tool's GitHub page where the contributers responded. ...
written 3 months ago by Cookie-san40

Latest awards to Cookie-san

Voter 12 weeks ago, voted more than 100 times.
Supporter 6 months ago, voted at least 25 times.

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