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**Pipeline recommendations:**
- [ ] are there any things that ENCODE does that we should do? anything that we do that ENCODE forgets? https://docs.google.com/document/d/1lG_Rd7fnYgRpSIqrIfuVlAz2dW1Va…
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Hi, in the graphShort session, is the required input file mitochondrial genome sequencing data or whole genome sequencing data?
I see a warnning:
Warning:` Please note that the SPAdes is not rec…
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Dear Adam, Gil, and other developers,
Thank you very much for developing and maintaining LDhat. I was hoping you could help me with a couple of questions, and I hope this is the right place for tha…
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### Is there an existing module for this?
- [X] I have searched for the existing module
### Is there an open PR for this?
- [X] I have searched for existing PRs
### Is there an open issue for this…
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Hi,
Thank you so much for your effort in developing and maintaining such a wonderful tool!
I am currently working on using WGS sequencing data for CNV calling, but I don’t have any normal samp…
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Hello,
I have some whole-genome sequencing BAM files of T-cell leukaemia. I was wondering how I can modify IgCaller to call T-cell receptor (TCR) rearrangements. Some guidance on how I can modify t…
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Hi,
I had ~37.8 million Illumina paired end sequencing reads (Plant whole genome with chloroplast and mito genome included). I tried assembling the Chloroplast genome where around 4.39 million read…
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I looked at the wiki but didn't understand it well.
Because it was different if the case is WGS from WIKI.
So please advise. I come up with the workflow as below for my aim at calling variant from…
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Hi there Kamil _et al.,_
First off, thanks so much for developing this amazing tool. I am having a pervasive problem with interpreting my smudgeplots - specifically, I am wondering whether they re…
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This issue is for keeping track of options for sequencing my DNA. Unfortunately, it seems all known methods require me to grant rights to my genes to the sequencing organization (including some copyr…