User: kwicher

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kwicher10
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Posts by kwicher

<prev • 5 results • page 1 of 1 • next >
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Comment: C: HMM and NGS mapping
... As I said, I would not have a reference sequence to map to, only a HMM profile of the sequences. ...
written 23 days ago by kwicher10
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Comment: A: HMM and NGS mapping
... Thanks all. RNAseq data would probably everything from 35bp to 250bp reads and the HMM profiles are predominantly more than 1kb, thus direct mapping does not work. I was thinking about doing something like that; first using the RNAseq data do de novo transcripts assembly and then using HMMER to id ...
written 4 weeks ago by kwicher10
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Comment: A: HMM and NGS mapping
... Yes, it is a good question and I cannot really go into the details but in general, I would not know the exact transcriptome but I would only have the HMM profiles based on the homologous sequences that were used to create the HMM profile. Thanks K ...
written 5 weeks ago by kwicher10
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Comment: A: HMM and NGS mapping
... The idea is that I would not map to the reference genome but tot a set of HMM profiles (describing the nucleotide sequences). ...
written 5 weeks ago by kwicher10
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HMM and NGS mapping
... Hello What would be the best tool to map short read RNAseq data to the reference transcript HMM profiles? One thing, the HMM profiles could possibly describe only a part of the actual transcripts. Thanks K ...
ngs hmm written 5 weeks ago by kwicher10

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