by tophat2 " tophat2 -p 8 -G genes.gtf genome file.fastq" command (gtf i think is the annotation flie 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 beddops tool or
bedtools multicov -bams yourBAMfile.bam -bed yourGenes.bed command by bed tool,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