Entering edit mode
9.5 years ago
Maguelonne
▴
20
I used this command line in bowtie:
bowtie -v 0 -m 1 ref file1.fastq file2.sam
and now I'm trying to convert the sam file I obtained:
samtools view -b -S file2.sam > file2.bam
and I get this error (even if I specify the -t ref.fa.fai
option):
[W::sam_read1] parse error at line 1
[main_samview] truncated file.
Here's the header of my sam file:
HWI-1KL110:149:HAUWDADXX:1:1101:1419:2097 1:N:0:ATCACG - MT 7644 TATCACCTTTCATGATCACGCC IEIFFIIIIIEEDDDDD8DDD? 0
HWI-1KL110:149:HAUWDADXX:1:1101:2046:2200 1:N:0:ATCACG + 17 57918633 TAGCTTATCAGACTGATGTTGACT CCCFFFFFHHDFHIIIIJJIJJJI 0
HWI-1KL110:149:HAUWDADXX:1:1101:3118:2245 1:N:0:ATCACG + 17 28444112 TGAGGGGCAGAGAGCGAGACTTT @@?DDD1D8CCDFE<FG6??CDE 0
Can someone help me?
Hi. Have you tried the following command ? :
(with -h option)
Yes, it doesn't work either.