Hi biostars,
By tophat2 (tophat2 -p 8 -G genes.gtf genome file.fastq) command (gtf I think is the annotation file and genome is the whole genome fasta), I produced a file named accepted_hits.bam which using
bam2bed < accepted_hits.bam | bedmap --echo --count genes.bed - > answer4.bed
command, by bedops tool or bedtools multicov -bams yourBAMfile.bam -bed yourGenes.bed command
by bedtools, I have a bed file now, like below
I 334 646 "YAL069W . + protein_coding CDS 0 exon_number "1"; gene_id "YAL069W"; gene_name "YAL069W"; p_id "P3633"; protein_id "YAL069W"; transcript_id "YAL069W"; transcript_name "YAL069W"; tss_id "TSS1128"; 2**
For example 2 reads have been mapped on gene YAL069W in 334-646 distance
but how I can know where each of these reads individually have been mapped? I mean how I can have a file in which I could see where each read individually has been mapped. For example these two reads in protein_coding (CDS) part, where have been mapped individually not just knowing that in 334 - 646, two reads have been mapped on gene YAL069W (not a distance in where a number of reads have been mapped).
Please if you have any idea, let me know
Thank you so much
