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teloclip-extract will write reads with terminal clipped-overhangs to fasta files. To aide in sanity checks we should include some metadata to the fasta header.
Proposed fields:
Anchor len: how much of the read is aligned to the ref sequence
Overhang len: how long is the overhang
Ref name: which sequence is it aligned to
Motifs : Motifs of regex patterns used in filtering (comma delim list)
Motif counts: Total count of motif matches in overhang (list matching order of motifs)
Other behaviour changes:
Sort fasta by overhang length
Include reference segment in output fasta (from earliest alignment start coord)
Log total read counts for each end of each reference sequence.
Print histogram of overhang depths
Log warning if unbalanced overhangs (i.e. most ends have 5 and one has 500 reads)
The text was updated successfully, but these errors were encountered:
teloclip-extract
will write reads with terminal clipped-overhangs to fasta files. To aide in sanity checks we should include some metadata to the fasta header.Proposed fields:
Other behaviour changes:
The text was updated successfully, but these errors were encountered: