count reads number in collapsed file

[lran2008]

Hi all,

I used bowtie to align a collapsed fasta file to the bovine genome and get a fasta file (mapped.fa) including all the mapped reads. But this mapped.fa is also a collapsed file. So how could I get the total reads number in mapped.fa, instead of the unique reads number?

Thanks.

Ran

[Heisman]

What do you mean by "collapsed"? Could you copy and paste the exact commands that were run?

[lran2008]

Hi Heisman, thanks for your reply. The collapsed file included the unique reads:

>1-30176523
TCAGTGCACTACAGAACTTTGT
>2-17234938
TTCAAGTAATCCAGGATAGGCT
>5-10273189
TACCCTGTAGAACCGAATTTGT
>6-10202799
TGAGATGAAGCACTGTAGCT
>7-7833696
TGAGATGAAGCACTGTAGCTCT
>8-7677783
TGTAAACATCCTCGACTGGA
>9-7403197
TGTAAACATCCTCGACTGGAAGCT
>10-5760993
TGGGGGGCCCAAGTCCTTCTGATCGAGGCC

So here I can get the number of total unique reads. But each unique read represents thousands of reads. How could I get the total number of the redundant reads in this file?

Thanks!