I do have multiple txt file for RNAseq read count, is it possible to generate a single txt file with the file name as column header;
txt file having read count like this: so first column is same in all files.
BGIOSGA000001 0 BGIOSGA000002 12 BGIOSGA000003 0 BGIOSGA000004 0 BGIOSGA000005 0 BGIOSGA000006 0 BGIOSGA000007 0 BGIOSGA000008 15
and txt file name are like this:
so I want out put like this:
Root_T3_S_R7_S56 Leaf_T2_F_R5_S8 BGIOSGA000001 0 4 BGIOSGA000002 12 0 BGIOSGA000003 0 3 BGIOSGA000004 0 2 BGIOSGA000005 0 4
I will be thankful for your help.
Kind Regards, Bioinfonext
You could have used
featureCountswhich does this when you feed it multiple BAM's on command line.
featureCounts options BAM1 BAM2 BAM3. Provide them in the same order you want to group them by so you you don't need to mess with columns afterwards.
I used HTSeq for read count and I am having like 60 read count txt files.
Consider redoing the counts with
featureCounts. You would be done with creating the count matrix in less time than it is going to take you to deal with 60 separate files :-)
I am having 60 read count txt file so should I keep adding all like you have shown with two files.