Tophat paired end read

[guzhi100]

Hi,
I am analyzing RNA-Seq data from one published paper.

Illumina Hiseq 2000 paired end reads. each end read is 101 bp.

I picked up one pair of reads to check the inner distance (required for Tophat) between these two reads, and found out that these two reads are actually much overlapped.

Then I realized that the size of the selected frangments might be around 133bp, which is why these two paired end reads have overlapping.

In this case, what should we type in for the inner distance between reads when using Tophat? "0" ?

hope you understand my question. Looking forward to hearing from you.

[Tahir Mujtaba]

As i am new to Bioinformatics, can anybody explain me single and paired end reads please?.

[guzhi100]

Tophat paired end read

Hi,
I am analyzing RNA-Seq data from one published paper.

Illumina Hiseq 2000 paired end reads. each end read is 101 bp.

I picked up one pair of reads to check the inner distance (required for Tophat) between these two reads, and found out that these two reads are actually much overlapped.

Then I realized that the size of the selected frangments might be around 133bp, which is why these two paired end reads have overlapping.

In this case, what should we type in for the inner distance between reads when using Tophat? "0" ?

hope you understand my question. Looking forward to hearing from you.

[pbluescript]

Tophat can do negative values, so put in the actual inner size between fragments, which will be negative if they overlap.