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Forum: Bioinformatics 04-02-2019, 08:16 PM
Replies: 678
Views: 184,114
Posted By seqmore
additional information: The outputs by both...

additional information:
The outputs by both sort methods are list below. Sorry to put so mach words here. In fact I have been tortured by this error for several weeks but cannot figure it out by...
Forum: Bioinformatics 04-02-2019, 07:43 PM
Replies: 678
Views: 184,114
Posted By seqmore
@GenoMax, Your suggestion is great! I uninstall...

@GenoMax, Your suggestion is great! I uninstall Samtools and reinstall 1.9. The samtools flagstat is working. Then I try output bam directly as you suggested, like this:
bbmap.sh...
Forum: Bioinformatics 04-02-2019, 07:50 AM
Replies: 678
Views: 184,114
Posted By seqmore
Thank you for your kindly replay @GenoMax. I...

Thank you for your kindly replay @GenoMax. I didnot specify ref= since I have copied the ref fold genereted by index building with bbmap to the current working directory. As I learned from your post,...
Forum: Bioinformatics 04-01-2019, 06:17 PM
Replies: 678
Views: 184,114
Posted By seqmore
RNAseq data analysis failed with BBMAP

Dear Brain,

BBMAP is great for mapping coverage and mapping speed. I have tried several times but failed. The versions of bbmap and samtools are 38.22 and 0.1.9, respectively. My data is RNA seq...
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