Fragment size of published single end RNAseq data

Question

[kojima.1aki]

Hello.

I'd like to use RSEM after STAR. Public RNAseq data was single ended, so we thought we should map our data to single ended.

However, the RSEM description reads as follows.

For single-end data, it is strongly recommended that the user provide the fragment length distribution parameters (--fragment-length-mean and --fragment-length-sd). For paired-end data, RSEM will automatically learn a fragment length distribution from the data.

For example, I found it impossible to know the fragment length for the following publicly available data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1547996

Is there no other way to do this without the option? Do I have to give up on having these two options?

If public data is Single End, how should I compare our own data?

Answer 1

[dsull]

Just give something reasonable for those two options (e.g. 200 for length, 20 for s.d.).

In practice, I’ve found that it really doesn’t make a big difference.