Biostar

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Comment: Finding out if a query sequence is present in a read library / bam file (blast a

Comment: Error: Your table upload failed because multiple BioSamples cannot have identica

Answer: Best way to detect CNV using WGS data

Comment: Setting up Aspera Connect (ascp) on Linux and macOS

Answer: Interleaved FastQ format

The Biostar Handbook. A bioinformatics e-book for beginners.

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Comment: Problem detecting indels by Estrella • 0

Thank you Pierre. I agree. But, for example, in position 2 IGV detects 140 deletions (total consensus sequences: 56452). I´ve tested with…

Comment: Scanpy Pearson residual PCA error by Arup Ghosh 3.0k

Seems like merging samples introduced some missing values.

Comment: Problem detecting indels by Pierre Lindenbaum 148k

just because you found one read with a deletion doesn't mean that a variant will be generated. Now, it doesn't explain why there is not any…

Comment: Error: Your table upload failed because multiple BioSamples cannot have identica by mibtisamnasar • 0

I have assigned unique IDs and attributes but still, it shows upload failed because multiple BioSamples cannot have identical attributes

Comment: Error: Your table upload failed because multiple BioSamples cannot have identica by mibtisamnasar • 0

![enter image description here][1] [1]: /media/images/9321c4d3-c07c-4f72-b443-29bd9b43

Comment: Best way to detect CNV using WGS data by Pierre Lindenbaum 148k

> CNVKit is designed for use with hybrid capture, including both whole-exome and custom target panels I think OP is asking for WGS data.

Comment: awk command for filtering by lieven.sterck 14k

yeah, you're right. Let's see where OP takes this (and I know better than to debate with you on awk topics, but I'm just in one of those m…

Answer: Best way to detect CNV using WGS data by colindaven 4.0k

CNVkit was relatively easy and results plausible on a large sample of about 70 exomes I had once. Results were not validated by the users b…

Comment: awk command for filtering by Pierre Lindenbaum 148k

it *should* work echo -e '1.1\n./2' | awk '($1!="./." && $1!="1/." && $1!="./1" && $1!="2/." && $1!="./2")' 1.1

Answer: Impute2 empty output for imputed SNPs by dongxinyu510 • 0

It should be that this chunk restricts the position of this chromosome without

Comment: awk command for filtering by lieven.sterck 14k

I don't think this will work as intended. When you use the 'negative' match ( != ) you more likely need to use the or operator ( || ) and …

Comment: Error: Your table upload failed because multiple BioSamples cannot have identica by Basti ▴ 670

What is not clear in the error message for you ?

Comment: Error: Your table upload failed because multiple BioSamples cannot have identica by andres.firrincieli 2.6k

Please, show us the sample submission table

Comment: DEXSeq unable to find an inherited method for function ‘NSBS’ for signature ‘"C by ta_awwad ▴ 320

> traceback() 11: stop(gettextf("unable to find an inherited method for function %s for signature %s", sQuote(fdef@gen…

Comment: Problem with extracting reverse-reverse read pairs by Pierre Lindenbaum 148k

Please create a [Minimal, Reproducible Example](https://stackoverflow.com/help/minimal-reproducible-example) to enable others to exactly r…

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