How can I see the assembly sequences in cufflinks output ?

[ericismax12]

Hi,everyone.

I want to use RNA-seq data to find NATs,so i use tophat and cufflinks to map and assemble reads.

my question: Does cufflinks output can see the assembled sequences??

I only can see the exons start and end.

How can I get the assembled sequences?? Thanks.

Eric

[hbt]

Cufflinks doesn't "assemble" the reads it merely annotates and quantifies the number of reads that map to each separate location of the genome e.g. an exon.
To view how the reads have mapped try IGV (http://www.broadinstitute.org/igv/)
which takes an indexed .BAM file from tophat

Hope this helps

[ians]

try gffread

[liweixie]

Tophat unmapped Bam

For tophat unmapped bam. I want to trim reads at 50bp. Anyone knows how to do this trim. Thank you!

[Zhenhao_Liu]

just i think

For tophat unmapped bam. I want to trim reads at 50bp. Anyone knows how to do this trim. Thank you!

是不是要编程删除50bp下的片段。我理解正确吗？
I think it should be done by writting a program of perl/c/c++, you can trim the sequence <50. Does it right?