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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
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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Recent Replies
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
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![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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