Dear Professor

computeMatrix reference-point --referencePoint TSS -p 15 -b 3000 -a 3000 -R sample.bed -S samole.bw --skipZeros -o sample.gz --outFileSortedRegions sample_genes.bed

about sample.bed
Is this bed file containing the range of genes, such as chr1 6642 11878 ?

May I ask if it is necessary to mark the positive and negative chains?
such as chr1 6642 11878 +
Will the program automatically recognize positive and negative chains？

If the input is in GTF format, just input the extracted transcript directly?
awk '$3 = "transcript" ' gtf > transcript.gtf

chr1 refGene transcript 6642 11878 . - . gene_id "rpl24"; transcript_id "NM_173235"; gene_name "rpl24";

computeMatrix reference-point --referencePoint TSS -p 15 -b 3000 -a 3000 -R transcript.gtf -S samole.bw --skipZeros -o sample.gz --outFileSortedRegions sample_genes.bed?

Thanks
Best regards
Jack