Comments (2)
Hi Dave,
The filename
field is not actually used so can safely be removed from the list on line 31. I have made this change in the develop branch (commit 64229af). If you could test this with your dataset, that would be very helpful.
As for reading in the PAF file, the PAF format doesn't specify a header row or rows. So this would lead to inadvertently excluding mappings from the script; therefore I have not included this change.
What command are you using to generate your mappings? We use:
$ minimap2 -x map-ont reference.mmi *.fastq > mappings.paf
Please let me know how these work for you.
Alex
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Hi Alex,
I'm mapping with a command similar to yours. But the top six rows look like headers, but it might actually be stderr content that is getting saved to my output file?
[M::mm_idx_gen::512.939*0.70] collected minimizers
[M::mm_idx_gen::591.117*0.72] sorted minimizers
[M::main::591.117*0.72] loaded/built the index for 195 target sequence(s)
[M::mm_mapopt_update::595.799*0.72] mid_occ = 694
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 195
[M::mm_idx_stat::597.579*0.72] distinct minimizers: 100167746 (38.80% are singletons); average occurrences: 5.519; average spacing: 5.607
11780e2c-77e3-42d3-b884-57d468156989 201 95 151 - chr12 133275309 23630798 23630852 40 56 0 tp:A:P cm:i:3 s1:i:40 s2:i:0 dv:f:0.0732 rl:i:0
c0a137db-7c95-4d12-aeb2-9871670baf0f 220 120 212 - chr4 190214555 155116878 155116975 45 97 1 tp:A:P cm:i:3 s1:i:44 s2:i:0 dv:f:0.0803 rl:i:122
c898b165-6b77-4100-aff1-1a77f9f8a071 271 49 140 - chr11 135086622 15677644 15677735 58 91 29 tp:A:P cm:i:6 s1:i:58 s2:i:0 dv:f:0.0835 rl:i:0
2cd0ee94-57da-46b8-ad86-07d0c5538d71 493 53 267 - chr11 135086622 73953443 73953652 87 215 10 tp:A:P cm:i:9 s1:i:87 s2:i:81 dv:f:0.0978 rl:i:0
This isn't a big deal, though. I have another issue but will start a separate ticket.
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