search

mapleforest / HaploMerger2

40 stars 6 forks source link

track back raw contig? #21

Open jun3234 opened 5 years ago

jun3234 commented 5 years ago

Great jobs with this programm. I just run two step A and B by set minOverlap with 999,999,999, when ran this "hm.batchB3.haplomerger bbv18wm_A. I got the output successfully. this sequence's name in 'Canu_1bs_A_alt.fa.gz' some like this:

Sc0000000 Sc0000001 Sc0000002 Sc0000003 this sequence's name in 'Canu_1bs_A_alt.fa.gz' , some like this: xpSc0002091 old_tig00005993;size:346208;start:0;length:2096 xpSc0002094 old_tig00003303;size:34220;start:32163;length:2057 xpSc0002102 old_tig00003259;size:289491;start:0;length:1911 xpSc0002111 old_tig00003035;size:241697;start:239894;length:1803 xpSc0002128 old_tig00003495;size:64333;start:0;length:1581 I don't know how get map between 'Sc0000001' and raw contig name 'tig***'. I check some intermediate file, including: image and, I still don't know how to get map, could you help me ?

mapleforest commented 5 years ago

xfScXX refers to a full original scaffold which has no allelic counterpart, or not paired up with other scaffolds.

xpScXX refers to a portion that is excised from an original scaffold, and has no allelic counterpart, or not paired up with other scaffolds.

About the mapping please check the output file "new_scaffolds", it is a self explained table file you can open it with Excel.

There are also description of this file in the manual.

Enjoy.