Cuffdiff Error Unrecognized file type (bam file)

[lwhitmore]

Hey All, Using the following command for cuffdiff I get the error
Error: cannot open file /home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/accepted_hits.bam for reading. Unrecognized file type


COMMAND
cuffdiff -o diff_out ./F6_Cuffmerge/LS/merged_asm/merged.gtf \ /home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/accepted_hits.bam \ /home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/F4_Alignment/LS/LS_XYM_AGG_THout/accepted_hits.bam


Any help would be greatly appreciated !

Leanne

[blancha]

As you posted the command, without any new lines, and two white spaces (one before and one after the backslash), the syntax is incorrect.

You need to add the new lines and remove the extra white space

cuffdiff -o diff_out ./F6_Cuffmerge/LS/merged_asm/merged.gtf \ 
/home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/accepted_hits.bam \ 
/home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/F4_Alignment/LS/LS_XYM_AGG_THout/accepted_hits.bam

If you're still experiencing problems, check that the file exists.

ls /home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/accepted_hits.bam

Also, check that the file is indeed a BAM file.

samtools view -h /home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/accepted_hits.bam | more

[lwhitmore]

Thanks Alot!