I have a hard-to-obtain sample sequenced. After removing the low quality reads, I found many orphan reads from each end. That is, the read in seq1 is good, but the corresponding read in seq2 has to be removed, vice versa.
I don't want to lose the information of these reads, so plan to map them to the reference using the tophat. I am seeking the best plan to go:
1. separately map them:
tophat genome_index_base seq1
tophat genome_index_base seq2
or
2. can I still treat them as paired end:
tophat genome_index_base seq1 seq2
please note that seq1 and seq2 each contains the orphan reads. But they were originally from the paired-end sequencing...
Thank you very much for any advice!
I don't want to lose the information of these reads, so plan to map them to the reference using the tophat. I am seeking the best plan to go:
1. separately map them:
tophat genome_index_base seq1
tophat genome_index_base seq2
or
2. can I still treat them as paired end:
tophat genome_index_base seq1 seq2
please note that seq1 and seq2 each contains the orphan reads. But they were originally from the paired-end sequencing...
Thank you very much for any advice!
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