Open nservant opened 1 year ago
First test version available with --processing pairtools
The options --keep_multi / --min_mapq / --min_cis_dist / --save_interaction_bam
have been managed
First version tested.
To further validate before release ... still need to find a way to use the options :
--min_insert_size
/ --max_insertisize
--min_restriction_fragment_size
/ --max_restriction_fragment_size
ext.args = { [
"(mapq1>${params.min_mapq} and mapq2>${params.min_mapq})",
params.min_cis_dist > 0 ? " and (abs(pos1-pos2) < ${params.min_cis_dist})" : '',
params.keep_multi ? " and ((pair_type=='UU') or (pair_type=='UR') or (pair_type=='RU') or (pair_type=='MM') or (pair_type=='MU'))" :
" and ((pair_type=='UU') or (pair_type=='UR') or (pair_type=='RU'))",
params.dnase ? '' : " and (abs(int(rfrag1) - int(rfrag2)) > 1)",
//params.min_insert_size > 0 ? " and ( (rfrag_end1 - r1pos) + (rfrag_end2 - r2pos)) > ${params.min_insert_size}" : '',
//params.max_insert_size > 0 ? " and ( (rfrag_end1 - r1pos) + (rfrag_end2 - r2pos)) < ${params.max_insert_size}" : '',
//params.min_restriction_fragment_size > 0 ? " -t ${params.min_restriction_fragment_size}" : '',
//params.max_restriction_fragment_size > 0 ? " -m ${params.max_restriction_fragment_size}" : '',
].join(' ').trim() }
Description of feature
Add a new paramater
--processing hicpro
or--processing pairtools
propose an alternative to
HiC-Pro
with the analysis protocol proposed by 'dovotail' and based onbwa-mem2
andpairtools
with the following steps :bwa-mem
(version 2 instead of 1)pairtools parse
- get valid ligation product / parameters--min_mapq
pairtools sort
- sorting pairsparitools merge
- merge pairspairtools dedup
- remove PCR dups / parameters--keep_dups
pairtools split
- generate pairs files (and final bam if useful ?)pairtools select
- filter pairspairtools stats
- generate final statsTo validate ;
--keep_multi
?pairtools
with--digestion, --restriction_site, --ligation_site, --chromosome_size, --restriction_fragments
parameters ?pairtools
? options--max_insert_size --min_insert_size --max_restriction_fragment_size --min_fragment_size
--dnase
withpairtools
?--min_cis_dist
) for--dnase
mode with--pairtools
Other ideas:
--dnase
option by--no_digestion
for DNAseq, microC, etc.