Hi everyone,
I am running a cuffdiff with GTF files from cuffmerge and SAM files from my mapped reads (CLC Bio). However, I've got error notification that my SAM files are not aligned. I searched through the web and found this:
Do Cufflinks and Cuffdiff support both BAM and SAM?
Yes. If a SAM is supplied, a message will be output that the file is not a valid BAM file. However, Cufflinks will recognize this and treat the file as a SAM. When using a SAM file, you should include a proper header or ensure that the reads are lexicographically by chromosome and then numerically by left position. You can accomplish this sorting with the command sort -k3,3 -k4,4n in.sam > out.sam.
As I am running from Galaxy website and not using the LINUX setting, what should I do to keep my analysis going using cuffdiff. Thanks.
Jasmine
I am running a cuffdiff with GTF files from cuffmerge and SAM files from my mapped reads (CLC Bio). However, I've got error notification that my SAM files are not aligned. I searched through the web and found this:
Do Cufflinks and Cuffdiff support both BAM and SAM?
Yes. If a SAM is supplied, a message will be output that the file is not a valid BAM file. However, Cufflinks will recognize this and treat the file as a SAM. When using a SAM file, you should include a proper header or ensure that the reads are lexicographically by chromosome and then numerically by left position. You can accomplish this sorting with the command sort -k3,3 -k4,4n in.sam > out.sam.
As I am running from Galaxy website and not using the LINUX setting, what should I do to keep my analysis going using cuffdiff. Thanks.
Jasmine
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