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There is a recurrent rearrangement found in all my calls for the DUX4 unknown partner. Is this a known false positive or am I misunderstanding something? Has this been found before?
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HI,
I am interested in checking a bat assembly using craq. I installed it using conda. Installation went fine, supposedly, but then it failed when I tried to run it using short-read data that I mappe…
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The kma seems to be ran with default parameters which means that the identity cut off is about 20% for sequence identity. Why is there custom no cut off for KMA?
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Dear team;
Thanks for providing those wonderful reference genome. It helps me a lot in my research. I met a problem that many of my reads could mapped to rrna region but was classified to not aligned…
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Hi Alex, I have some issues with a data that I have receipt from collaborators, I have normally worked with Smart-seq plate based protocols, but this samples are 10x, and I don't have a lot of informa…
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Dear Dobin,
I'm using STAR to map the Ribo-seq results to a genome. I ran the program with and without the "--twopassMode Basic" parameter, and found that by using the 2-pass mode, the alignment ra…
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Dear @tsackton @erikenbody and other developers,
Thanks for developing such a capable and interesting tool!
I am looking to deploy snpArcher for population genomics projects but the starting dat…
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I have a question concerning the recommended workflow.
I used short reads to create the input VCF file and the ont long reads in whatshap.
I used the pipeline below but my haplotype a nearly the s…
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### Description of feature
I'm noticing a lot of multi-mapping reads and those unmapped as 'too short'. Some of this is just down to the short read lengths I guess, but we should try to add some ST…
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I got error message"EXITING because of FATAL ERROR in reads input: short read sequence line: 0
Read Name=@HWI-D00289:135:C4U3VACXX:3:2316:6629:26242
Read Sequence====
DEF_readNameLengthMax=50000
D…