User: kwicher

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kwicher10
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8 months ago
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10 months ago
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Posts by kwicher

<prev • 9 results • page 1 of 1 • next >
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Comment: A: How to get hold of the gff files for RepeatMAsker annotated human genome
... Thank you. Just a comment. It spit out the following message at the beginning: `Use of uninitialized value $ENV{"DP_GFF"} in uc at cnv_repmask2gff.pl line 50.` Though seems to be doing what it is meant to. ...
written 8 months ago by kwicher10
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How to get hold of the gff files for RepeatMAsker annotated human genome
... Hello How to get hold of the precomputed RepeatMasker gff files for human genome? Thanks K ...
genome gff repaetmasker human written 8 months ago by kwicher10
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Comment: C: HMM and NGS mapping
... These are 10s of millions short reads RNA-seq data and HMM profiles are several 100s bp long Would that work? ...
written 8 months ago by kwicher10
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Comment: C: HMM and NGS mapping
... No I do not have access to that. ...
written 8 months ago by kwicher10
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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 9 months 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 10 months 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 10 months 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 10 months 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 10 months ago by kwicher10

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