Read counts by coordinates-Chromosome

Question

[annaA]

Hello,

I have a RNAseq dataset -BAM files from chimps and a BED file with chromosome- coordinates for sequences of interest, I am looking for a tool or script which I can use to count these sequences by using the coordinates-chromosome info in my BAM files and produce a expression matrix - in the same manner as FeatureCounts

Any help will be super appreciated, A.

Answer 1

[GenoMax]

If you have a BED file then creating a simple annotation format (SAF) file will be easy to do. featureCounts can use SAF format files to do the counting. SAF format is described in the subread/featureCounts manual.

[annaA]

Perfect thanks for the help, I just checked it! I have seen this part but it wasn't clear to me that you can use the coordinates

Many thanks