strand-specific read countin with featureCounts

Question

[Bioiris]

hi,

I wanted to quantify transcripts of 20 files bam I second flight featureCount, the data are paired-end but it is unclear whether or not reversely stranded, I tested both options to see

featureCounts -p -T 4 -s 1 -t exon -g  gene  -a input.gtf  -o output_S1  input1.bam input2.bam input3.bam ......input20.bam

featureCounts -p -T 4 -s 2 -t exon -g  gene  -a input.gtf  -o output_S2  input1.bam input2.bam input3.bam ......input20.bam

i have the results in 2 files S1 and S2

to confirm, i sought the gene BCAT

$ grep -i BCAT output_S1.txt
BCAT2   chr19;chr19;chr19;chr19;chr19;chr19;chr19;chr19;chr19;chr19;chr19;chr19;chr19   49298319;49299685;49299835;49300194;49300448;49302932;49303238;49303444;49309774;49310257;49311013;49314066;49314241    49298721;49299759;49299975;49300279;49300590;49303095;49303357;49303554;49309974;49310331;49311493;49314178;49314320    -;-;-;-;-;-;-;-;-;-;-;-;-   2193    9   6   3   8   14  4   19  2   7   14  2   10  24  16  17  3   40  15  58
BCAT1|BCAT1 chr12;chr12;chr12;chr12;chr12;chr12;chr12;chr12;chr12;chr12;chr12;chr12;chr12   24962958;24982757;24985657;24989445;24995016;25002720;25031464;25034235;25047209;25054748;25054897;25055881;25101861    24970983;24982831;24985797;24989530;24995158;25002883;25031583;25034345;25047409;25054819;25055322;25056009;25102393    -;-;-;-;-;-;-;-;-;-;-;-;-   10227   47  207 112 149 52  49  347 79  339 68  82  282 554 307 290 281 241 1068    600 1807



$ grep -i BCAT  output_S2.txt
BCAT2|BCAT2 chr19;chr19;chr19;chr19;chr19;chr19;chr19;chr19;chr19;chr19;chr19;chr19;chr19   49298319;49299685;49299835;49300194;49300448;49302932;49303238;49303444;49309774;49310257;49311013;49314066;49314241    49298721;49299759;49299975;49300279;49300590;49303095;49303357;49303554;49309974;49310331;49311493;49314178;49314320    -;-;-;-;-;-;-;-;-;-;-;-;-   2193    7   8   6   9   6   13  9   1   18  12  1   4   29  15  18  5   47  11  71
BCAT1|BCAT1 chr12;chr12;chr12;chr12;chr12;chr12;chr12;chr12;chr12;chr12;chr12;chr12;chr12   24962958;24982757;24985657;24989445;24995016;25002720;25031464;25034235;25047209;25054748;25054897;25055881;25101861    24970983;24982831;24985797;24989530;24995158;25002883;25031583;25034345;25047409;25054819;25055322;25056009;25102393    -;-;-;-;-;-;-;-;-;-;-;-;-   10227   46  255 108 144 37  50  296 84  332 61  72  272 598 260 294 271 246 997 626 1644

I basically have the same quantifications in both files is it normal ? normally we found quantifications High in a file and not the in the other?

Thank you;

Answer 1

[Devon Ryan]

The numbers suggest that the data is unstranded.

[Bioiris]

I thought of that too and has inferexperiment confirm that's unstranded data thank you