I used cufflink (v2.0) to analyze my RNA-seq data.
It turned out there was problem with the gene fpkm and isoform fpkm.
The coverage, FPKM, FPKM_conf_lo, and FPKM_conf_hi are zero.
Also, I ran the tophat first and got a BAM file. But the program reported that 'File ./SC/accepted_hits.bam' doesn't appear to be a valid BAM file’.
The reads of my RNA-seq dataset are single-end and are in length of 49nt. My reference genome is consisted of 410,030 contigs
I remember cufflink worked for my zebra fish RNA-seq dataset which is single-end and has reads of 100nt.
Here is the command I used
cufflinks -p 10 -o controlCufflinkOut -g Pvirgatum_202_gene.gff3 ./SC/accepted_hits.bam
I also tried the parameter --library-type fr-firststrand. I got the same result.
Could someone give me some suggestion on this problem?
is there similar tool to replace cufflink?
It turned out there was problem with the gene fpkm and isoform fpkm.
The coverage, FPKM, FPKM_conf_lo, and FPKM_conf_hi are zero.
Also, I ran the tophat first and got a BAM file. But the program reported that 'File ./SC/accepted_hits.bam' doesn't appear to be a valid BAM file’.
The reads of my RNA-seq dataset are single-end and are in length of 49nt. My reference genome is consisted of 410,030 contigs
I remember cufflink worked for my zebra fish RNA-seq dataset which is single-end and has reads of 100nt.
Here is the command I used
cufflinks -p 10 -o controlCufflinkOut -g Pvirgatum_202_gene.gff3 ./SC/accepted_hits.bam
I also tried the parameter --library-type fr-firststrand. I got the same result.
Could someone give me some suggestion on this problem?
is there similar tool to replace cufflink?
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