Entering edit mode
2.9 years ago
mrs97
•
0
I've been working to process RNAseq data and I've used hisat2 to align my reads to the reference genome. When I take those output files and put them into HTSeq-count using the below code, I get a count matrix but the columns lack headers so I can't tell which column is associated with each of the 24 libraries. Does anyone know how to add labels to each column that correspond to their correct library?
The PBS script I used for HTSeq is: htseq-count -m union -s no -i ID *_hisat2_out S_B_combined.gff > HTSeq_output.txt
The head of HTSeq_output.txt looks like this:
ANN00001-RA:exon:43 9 6 19 9 5 13 15 13 20 7 12 7 14 3 11 10 13 19 17 11 17 6 8 8 8
ANN00001-RA:exon:44 24 9 23 27 12 20 24 15 17 21 21 23 13 11 30 6 34 16 34 13 22 12 20 24 17
ANN00002-RA:exon:3 43 108 21 249 73 106 27 68 38 145 8 108 18 111 18 78 50 245 30 158 37 324 49 196 75
ANN00002-RA:exon:4 123 512 69 786 254 377 97 279 98 486 33 359 54 406 74 316 174 833 77 596 126 1126 214 781 295
ANN00003-RA:exon:68 7 72 7 109 2 56 20 66 15 58 16 150 11 41 6 53 13 44 8 39 15 46 10 102 26
ANN00003-RA:exon:69 9 85 7 102 5 71 8 65 11 78 11 191 7 47 5 44 23 51 5 45 14 78 14 145 42
ANN00003-RA:exon:70 31 197 19 220 11 150 26 156 23 137 37 341 28 118 17 83 34 108 18 100 27 141 29 300 69
ANN00003-RA:exon:71 0 19 3 21 3 12 4 16 9 15 4 35 3 18 0 9 5 14 2 13 2 7 3 26 6
ANN00003-RA:exon:72 2 49 7 51 3 30 6 40 8 35 2 76 5 23 4 26 4 24 5 22 8 26 5 65 22
ANN00003-RA:exon:73 11 127 8 124 2 82 12 93 13 68 18 183 17 65 0 61 18 50 4 59 19 83 8 173 43
Much thanks in advance!
