[miso-users] Short paired end or long single ends?

[Leila Alieh]

Dear all,

I am new to MISO and I am not a bioinformatic expert. I would like to use
MISO for some alternative splicing analysis but i have some questions:

1)I have data from paired end sequencing 100 bp. Unfortunately the whole
set of reverse reads had to be trimmed to 66 bp after quality control. I
know that MISO requires reads of the same lenght. My question is: is is
better to trim all the reads to 66 bp (pretty short for alternative
splicing decetion), discarding some part of the reads with good quality and
use MISO in paired-end mode, or would it be better to split the reads and
do the analysis only with the forward reads (all of 100 bp) in single-end
mode?

2) I read in the manual that the bam files must be sorted and indexed
before running MISO. After those processes the bam files have extension
bam.bai. However in the examples reported in the MISO Manual I find only
input as simply .bam or sorted.bam, never in bam.bai. Which input should I
use?

Thanks in advance!
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