Hello,
I have multiple fastq files. I want to use tophat for the alignment and use cufflink to get the annotation. Because the memery limit, I need to process one file each time.
My question is:
do I need to merge the SAM/BAM files of tophat before using cufflink (1), or can I use cufflink for each SAM/BAM file and then use cuffmerge to merge the annotation files (2) ?
(1)
tophat file1.fq --> cufflink file1.sam
tophat file2.fq --> cufflink file2.sam
cuffmerge file1.gtf file2.gtf
(2)
tophat file1.fq
tophat file2.fq
sammerge file1.sam file2.sam
cufflink merge.sam
Thank you very much!
I have multiple fastq files. I want to use tophat for the alignment and use cufflink to get the annotation. Because the memery limit, I need to process one file each time.
My question is:
do I need to merge the SAM/BAM files of tophat before using cufflink (1), or can I use cufflink for each SAM/BAM file and then use cuffmerge to merge the annotation files (2) ?
(1)
tophat file1.fq --> cufflink file1.sam
tophat file2.fq --> cufflink file2.sam
cuffmerge file1.gtf file2.gtf
(2)
tophat file1.fq
tophat file2.fq
sammerge file1.sam file2.sam
cufflink merge.sam
Thank you very much!
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