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loneknightpy / idba

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Question: Record which reads map to which contigs? #6

Open fwhelan opened 9 years ago

fwhelan commented 9 years ago

Good morning, and thank you for making IDBA available! I have a quick question which I hope you don't mind me posting here: Is it possible to record which reads map to a particular contig with IDBA_UD? I know that I could use something like BWA to map reads back to the contigs produced with IDBA_UD, but was wondering if it is possible to save this information as the contigs are being produced.

Thanks! --Fiona

fwhelan commented 8 years ago

Question retracted. I was using -l instead of -r, which from responses to issue #11, tell me is not what I should have been doing. With -r I at least get read counts, but not a record of specific reads.

fwhelan commented 8 years ago

Wait- is the read_count output in the header of contig.fa really the number of reads that contribute to that contig? Or is it a kmer_count as is mentioned in this post from years ago? https://groups.google.com/forum/#!topic/hku-idba/5z696QgAooM

mooreryan commented 7 years ago

The read_count in the output fasta file does look like it is the count of kmers, NOT the count of reads.

(I'm basing this assumption off the fact that the value that gets printed in the output fasta file is the same one that is used for vertex counts in the hash graph.)