matlock bam2 juicer #13
Description
Hi, I met a problem.
When I use this command: "matlock bam2 juicer sample.bwa_aln.bam out.links.txt", I get a result file out.links.txt.
But this file has no sequence, so when I use run-assembly-visualizer.sh to get the .hic file, some problems happened.
the out.links.txt :
16 ptg000376c 16496 0 0 ptg000376c 16269 1 1 - - 1 - - -
0 ptg000044l 1718493 0 16 ptg000044l 1718671 1 1 - - 1 - - -
0 ptg000020l 16093918 1 0 ptg000167l 1680688 0 1 - - 1 - - -
Maybe I missed some steps?
Here is my file
genome.fa
ptg000001l
CCTAACCCTAACCCTAACCCCTAACCCTAACCTAACCTAACCCTAACCCTTACCCTAACC
CTAACCTAACCTAACCTAACACTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAA
CCCTAACCCTACCCTTACCATACCTAACCTAACCCTAACCCTAACCCTAACCCTAACCAA
sample.sort.bam
E250065638L1C001R00300000444 87 ptg000376c 16497 29 79M71S = 16270 -306 TGTCTGCAACGAGCGTTCAGAAGAGAAATTGGGTGATGGGTCGGAATGTCAGTCCTCGTTGTTTTGACGTATGGAGAATTGGTACCACTATTAGTACGAGAATGGAGAATAGAAGGGCTAGGACTCCTCCGAGTTTGTTTGGAATTGATC GIGIGIICCIICIIIGGICICCICICCCGGIIIGICGIIIGIIICCGIGICIGIIGIIGGIGGGGICIIGCGIICICCGGIIGCIICIGCGGCIGCIICICCGIICICCGCICCIIIIGCIICIGIIGIIICIGGGIGGGIICCGGICGI XT:A:M NM:i:0 SM:i:29 AM:i:29 XM:i:0 XO:i:0 XG:i:0 MD:Z:79
E250065638L1C001R00300000444 163 ptg000376c 16270 29 150M = 16497 306 CTTTTTTCTGGCGCTAGGGAGGAATTTAACCTCCGATCTTCGGATTACAAGACCGATGCTTTAATTTAAGCTACTAGGGCAAGCTCATTCTAGGGCTTTATTCTCTAATCACCCTGCCAGTGGTATAAGTATTAGGAATAATGCGAAGTA IEEEEEEIEIIB;CDCIFIC@DACEEECCIIEIIDCEIEEICFCDECICCICI9ICBIGEDECCCEECCHIECIDC=ABICCIFEIC@EIECIB9HEDECDEIEIECCCICIIHEIIICIBI6ACDCCIBCEDCIICCDCCBI;ICCH?C XT:A:U NM:i:0 SM:i:29 AM:i:29 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:150
genome.assembly
ptg000023l 1 25304361
ptg000042l 2 4781932
ptg000671l 3 33829
ptg000306l 4 343936
ptg000624l 5 22770