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Magdoll / SQANTI2

SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
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How to generate a short read expression file? #44

Closed qoiopipq closed 4 years ago

qoiopipq commented 4 years ago

I've a question about using RSEM to quantify Iso-Seq collapsed long reads by RNA-seq short reads, then use it as a short read expression file for running SQANTI2. Sorry if here is not the place to discuss it. As SQANTI paper stated that it can take Iso-Seq + RNA-seq as input. My understanding is to use the Iso-Seq collapsed long transcripts as reference then map short reads against using RSEM (or other tools). According to RSEM, it requires reference sequences using (rsem-prepare-reference command). I tried to run this command to build collapsed long reads as the reference, but it didn't work. For all the options in RSEM preparing reference step, I don't think which one should be used. If anyone can provide the commands or options that will be great.

For the Iso-Seq pipeline, I've GMAP aligned files, ToFu collpased transcripts, and for RNA-seq, paired end reads.

Cheers!

Br1anChou commented 4 years ago

Hi @qoiopipq @Magdoll , I have the same problem. How did you solve it? I used the software RSEM. Best!