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Recent Replies
Comment: add 1/2 to fastq header
by
barslmn
▴
90
This can be achived with awk too.
zcat myfastq.gz | awk '/^@/{$0=$0"TexIWantToAdd"} 1'
Comment: CNVKit does not output all the accessible regions in the targets bed file
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barslmn
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That kind of mismatch is the usual suspect. What is the result if you manually create the bed file and supply it with `--targets` argument?…
Comment: Transform Data into DNA picture
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barslmn
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These rsids are identifiers for specific alleles. Genotypes here indicates the alleles observed at that locus. https://en.wikipedia.org/wik…
Comment: Mapping all 32-mers within Hamming Distance = 3
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@genomax Thank you so much for this response! I think I misspoke (and learned the difference btwn alignment vs. mapping https://www.biostar…
Comment: Download peptide sequences from NCBI using python
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Ram
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A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: Manually order the set fails in UpsetR
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swbarnes2
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The top one has them in reverse alphabetical order, your selected species list is in alphabetical order.
Comment: How to find rna strand direction before alignment?
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KoppesEA
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Right, I mean you can't get strandedness without aligning. The first two answers just align a subset and align reads and the second actuall…
Comment: Genotyping
by
kiran
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0
thank you so much, i will look into local assembly and also the link provided.
Actually i'm using tandem repeats genotyping tool, called G…
Comment: add 1/2 to fastq header
by
Mensur Dlakic
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There is no global header in FASTQ files, only headers of individual reads. I think it is a safe assumption that adding to individual heade…
Answer: How to calculate log2foldchange in python?
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Jack Tierney
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As Matthias answered above, there are likely 0s in your arrays that are turned into Nans by `np.divide()`. This is because the default repl…
Comment: add 1/2 to fastq header
by
LChart
1.5k
This will add /1 /2 to the individual reads....which might be what the user actually wants?
Answer: How to calculate log2foldchange in python?
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Matthias Zepper
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The most likely explanation is, that your data contains zeros. This would return `Inf`, since you can't compute a log value of 0.
[The typ…
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Hi. Thank you for the tips. The accepted answer resolved my issue. It was due to the wrong use of quotes.
Comment: Genotyping
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LChart
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I'm not sure how often **realignment** is used specifically any longer; many callers are using local **assembly**. The assembled haplotypes…
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