Hello.
I am now trying RNA-seq data analysis using Tophat-Cufflinks process.
I have two human RNA-seq data from Solexa sequencing (single-end) and my goal is comparing gene expression level and alternative splicing patterns of each data.
Without any option, I ran tophat with UCSC hg19 and obtained two accepted_hits.sam files.
Then, through cufflinks and cuffcompare, single gtf file, stdout.combined.gtf file is made and used for cuffdiff along with two sam files.
After cuffdiff run, I could see several files such as gene_exp.diff.
My question is below.
When I open the cuffdiff results files, I can not find gene information as below.
How can I get gene information?
I am now trying RNA-seq data analysis using Tophat-Cufflinks process.
I have two human RNA-seq data from Solexa sequencing (single-end) and my goal is comparing gene expression level and alternative splicing patterns of each data.
Without any option, I ran tophat with UCSC hg19 and obtained two accepted_hits.sam files.
Then, through cufflinks and cuffcompare, single gtf file, stdout.combined.gtf file is made and used for cuffdiff along with two sam files.
After cuffdiff run, I could see several files such as gene_exp.diff.
My question is below.
When I open the cuffdiff results files, I can not find gene information as below.
Code:
test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant XLOC_000001 - chr1:763004-764484 q1 q2 NOTEST 0 9.91482 2.13631e-314 1.79769e+308 0 no XLOC_000002 - chr1:895380-897112 q1 q2 NOTEST 6.56765 2.24444 -1.0737 1.38868 0.16493 no XLOC_000003 - chr1:897214-901465 q1 q2 NOTEST 11.9247 2.23374 -1.67493 4.67081 3.00007e-06 no XLOC_000004 - chr1:908878-909553 q1 q2 NOTEST 0 4.13402 2.14785e-314 1.79769e+308 0 no
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