How to label columns in HTSeq output

How to label columns in HTSeq output

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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!


RNAseq


HTSeq


counting


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