Sorry friends,
Below we can see few rows of a bed file from bowtie2. Column one is the name of genes, columns two and three are the position where the read has been mapped (start and end)..and as you see gene YAL001C is being repeated (the times this gene has been repeated is equal to the number of reads that have mapped on the different places on this gene)
YAL001C 0 31 SRR1944914.13670510 42 +
YAL001C 0 31 SRR1944914.14245831 42 +
YAL001C 0 31 SRR1944914.14846638 42 +
YAL001C 21 49 SRR1944914.16464709 42 +
YAL001C 34 64 SRR1944914.16452509 42 +
YAL001C 39 68 SRR1944914.9573160 42 +
YAL001C 41 72 SRR1944914.10936494 42 +
YAL001C 47 78 SRR1944914.3091079 42 +
YAL001C 51 81 SRR1944914.14101000 42 +
YAL001C 63 94 SRR1944914.6961904 42 +
YAL001C 64 94 SRR1944914.1613580 42 +
YAL001C 81 112 SRR1944914.6321368 42 +
YAL001C 87 117 SRR1944914.15157073 42 +
YAL001C 102 133 SRR1944914.6375363 42 +
YAL001C 110 142 SRR1944914.3776687 42 +
YAL001C 110 140 SRR1944914.8299121 42 +
YAL001C 110 140 SRR1944914.10247842 42 +
YAL001C 123 153 SRR1944914.17267226 42 +
YAL001C 153 184 SRR1944914.11895906 42 +
YAL001C 162 191 SRR1944914.8661898 42 +
YAL001C 162 193 SRR1944914.15558858 42 +
YAL001C 183 214 SRR1944914.1191651 42 +
Anyway I am with yeast and I used tophat2 using ensemble gtf file and so on)...many days I am trying to have such a bed by the tophat2 bam.file but I could not yet...a file in which the column one is the gene name and repeated as how many as reads have been mapped on and columns two and three are the start and the end of mappig of each read
Do you have any idea to have such a file?
Thank you
Oh Andrew come on. I mean I produced a sam then bam then bed
I mean 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 namedaccepted_hits.bam
which usingcommand, I have a bed file now....but adviser asking me to have a file like what I pasted above
but what I have is like below:
anyway thank you