Need urgent help for Tophat + Cufflinks !!!

[fangquan]

Hi folks,

I'm running tophat (tophat -o output_dir a_ref a.fq) for alignment and cufflinks (cufflinks -o output_dir accepted_hits.bam) for assembles transcripts. The reads are single-end, 40-bp long.

This is my command line:
tophat -o tophat_60PO ./hg19 ./60PO.fastq
cufflinks -o cufflinks_60PO tophat_60PO/accepted_hits.bam

The results:
Step 1:
$ ls -l tophat_60PO
-rw-rw-r-- 1 fangquan fangquan 1104315390 Aug 4 09:45 accepted_hits.bam
-rw-rw-r-- 1 fangquan fangquan 52 Aug 4 09:35 deletions.bed
-rw-rw-r-- 1 fangquan fangquan 54 Aug 4 09:35 insertions.bed
-rw-rw-r-- 1 fangquan fangquan 52 Aug 4 09:35 junctions.bed
-rw-rw-r-- 1 fangquan fangquan 70 Aug 4 05:54 left_kept_reads.info
drwxrwxr-x 2 fangquan fangquan 4096 Aug 4 09:04 logs


The results are weird, deletions.bed, insertions.bed, and junctions.bed are EMPTY files, with only track name.

#############################################
#############################################
Step 2:
$ls -l cufflinks_60PO
-rw-rw-r-- 1 fangquan fangquan 129 Aug 5 14:53 genes.fpkm_tracking
-rw-rw-r-- 1 fangquan fangquan 129 Aug 5 14:53 isoforms.fpkm_tracking
-rw-rw-r-- 1 fangquan fangquan 0 Aug 5 14:53 transcripts.gtf


The results are weird again, three files are all EMPTY. And I tried all ten samples but all end up weird results.



Can anyone help me figure out what's going wrong ? I have ten samples and all of them have the same weird results. Waiting for your replies !

Thanks,
Quan

[evergreen]

maybe you can change the parameter --segment-length and try the programs again