Hello, I ran bismark with paired-end reads.
According to the manual, the result SAM file should had contained both read 1 and 2 sequences, mapping qual, and etc. But I didn't get them both.
I used TrmGalore for adapter removal with the paired-end option to make sure both mates were paired.
Command I used :
Here's some examples from my result,
Thank you.
According to the manual, the result SAM file should had contained both read 1 and 2 sequences, mapping qual, and etc. But I didn't get them both.
I used TrmGalore for adapter removal with the paired-end option to make sure both mates were paired.
Command I used :
Code:
bismark --non_directional --bowtie2 -p 8 -N 1 -L 10 ../mm10/ -1 MEF_R1_val_1.fq -2 MEF_R2_val_2.fq
Code:
HISEQ:284:HAK1MADXX:1:1101:1451:2148_1:N:0:CGATGT 99 chr7 48002502 23 101M = 48002628 227 AAATGTGGTATATTTATATAATGGAGTATTATTTAGTTATTAAAAAGAGTGTATTTATGAAATTTTTAGTTAAATGGATGGATTTGGAGGGTATTATTTTG C@CFFFEFFHHHHJJIJIJIJIJJJJJHJJJJJJJIJIJIIIIIJHIEGBDEGHIJGJJJIGJJJJJJIJJIHIIJJHHGGGHIJJHAEFF5@@D>CEEEA NM:i:19 MD:Z:10C2C2C1C9C2C1C2C11A15C0C3C0C11C0C7C2C2C0C2 XM:Z:..........h..h..h.h.........h..h.x..h...........................hh...hh...........hx.......h..h..hx.. XR:Z:CT XG:Z:CT HISEQ:284:HAK1MADXX:1:1101:1451:2148_1:N:0:CGATGT 147 chr7 48002628 23 101M = 48002502 -227 ATTTATATAATATGTATTTATTGATAAGTGTTTATTAGTTTAAAATTTAGGATATTTAAGATATAAGATATAATTTATTAAATATATGAAATTTAAGAAGA FDCHHHHHHHIIGGIGDGFGGIHDIHJJJHIJJJJJIIIIJJHIIEJJJJJJIGGIJJIJJJJJIHFIJJJJIHHC,IJIGJJIJJJJHHHHDDFFFFCCC NM:i:23 MD:Z:1C1C1C1C8C1C1C9C7C0C0C5C7C0C0C13C5G0C4C1C6C1C5A1 XM:Z:.h.h.h.h........h.h.x.........h.......hhh.....h.......hhh.............h......h....h.h......h.h....... XR:Z:GA XG:Z:CT
Comment