Sort and convert the SAM files to BAM
When I going to convert sam to bam file it's showing error like this.
prashant@prashant-07:~/Desktop/histates$ samtools sort -@ 8 -o SRR087416_chrx.bam SRR087416_chrx.sam
sort: invalid option -- '@'
open: No such file or directory
[bam_sort_core] fail to open file 8
prashant@prashant-07:~/Desktop/histates$
Thank you
• 2,843 views
•
link
updated
by
Ram
•
written
by
amitunited0532 •
•
written
by
amitunited0532 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Samtools sort error: [pretty_header] invalid header
written by Ondina •
-
samtools view: failed to open for reading , samtools sort :can't open file
written by maria •
-
Problems with alignment in bash mode with hisat2
written by Peter •
-
samtool sort
written by jiahui •
-
How to rectify error while sorting the sam file
written by sunnykevin97
-
Sort bam file by coordinates using samtools
written by Shahzad •
-
Mapsplice 2 error
written by amitunited0532 •
-
htseq-count: error when reading beginning of SAM/BAM file.
written by cgias •
-
Help with Samtools
written by oma219 •
-
error from samtools view -h
written by jolin0701-dy
Try this
when i m giving command it's shows error like this.......
Have you seen my question? Without knowing the version of
samtoolsit's quite hard to help.Thanks.
fin swimmer
Samtools version: 0.1.9 (r783)
Hello amitunited0532,
this version is nearly 8 years old. Current version is 1.9. Update is realy necessary. Download and install instructions are here.
fin swimmer
Thank you for giving your valuable time, I have updated samtools and now it's working properly.
Hello amitunited0532,
check your version of samtools with
samtools --versionThe@option was introduced in version 1.0.fin swimmer