- GetReadLengthPerGene takes Gene IDs and determines the read length distribution for its transcripts per sample, from both transcriptome and genome alignment SAM files.
- It requires the mm10_gene_list.txt file to see which transcripts belongs to which gene, the mm10_transcript_positions.txt file to check the strand and the positions of the transcripts, and the SAM files.
- The script creates one file per transcript, the read lengths in the first column, and the number of reads with this length per sample in the next columns.
- It also creates a summary file, with all read lengths summed up.
- Updated mm10_transcript_positions.txt file by *manually* adding four transcripts to this list, needed for the lincRNA read length check.