Dear all,
I am analyzing iClip data and i have some questions concerning reads annotation with bowtie.
The data that i have to analyse have been pre processed by someone. He returns me .bed (ex : chrX 111265 111278) files with the chromosome and the coordinates of each read that have been sequenced. So i use bedtools (fastaFromBed) to get sequence from coordinates.
Then, i align all the reads on all the transcripts of D.melanogaster with bowtie. ( bowtie --norc -v 1 -t dmel-all-transcript -f mydata.fasta ).
But i have a problem : some reads wich where mapped to the chromosome X (for example) have been annotated on a transcript that came from the chromosome 2 (for example), and this is not normal !!
Someone have an idea to solve this problem ? Maybe i forget an option in Bowtie ?
Thanks in advance for your reply,
I am analyzing iClip data and i have some questions concerning reads annotation with bowtie.
The data that i have to analyse have been pre processed by someone. He returns me .bed (ex : chrX 111265 111278) files with the chromosome and the coordinates of each read that have been sequenced. So i use bedtools (fastaFromBed) to get sequence from coordinates.
Then, i align all the reads on all the transcripts of D.melanogaster with bowtie. ( bowtie --norc -v 1 -t dmel-all-transcript -f mydata.fasta ).
But i have a problem : some reads wich where mapped to the chromosome X (for example) have been annotated on a transcript that came from the chromosome 2 (for example), and this is not normal !!
Someone have an idea to solve this problem ? Maybe i forget an option in Bowtie ?
Thanks in advance for your reply,