MapSplice2 circRNA output

Question

[Grouse]

Hi everyone! I am trying to run MapSplice2 with paired-end RNA-Seq data to characterise circRNAs. I can get it to run but my output for circRNAs is empty.

Also, the website (http://www.netlab.uky.edu/p/bioinfo/MapSplice2) is down so I am unable to access the full manual.

Here's part of my PBS script:

module load python

for file in /srv/scratch/ID/Mouse_data/trimmomatic_results_unzipped/*R1_paired*; do r2=${file/R1_paired.fastq/R2_paired.fastq}; python /srv/scratch/ID/mapsplice2/MapSplice-v2.1.8/mapsplice.py -p 16 --gene-gtf /srv/scratch/ID/mouse_genome/test_index/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf -o /srv/scratch/ID/Mouse_data/mapsplice2_results/ --fusion --fusion-non-canonical --min-fusion-distance 200 -c /srv/scratch/ID/mouse_genome/test_index/Mus_musculus/UCSC/mm10/Sequence/Chromosomes/ -x /srv/scratch/ID/mouse_genome/test_index/Mus_musculus/UCSC/mm10/Sequence/BowtieIndex/ -1 $file -2 $r2; done

If anyone could help that would be much appreciated! Thanks.

[archana.bioinfo87]

Hi, Mapsplice2 site is working

http://www.netlab.uky.edu/p/bioinfo/MapSplice2

Thanks

[archana.bioinfo87]

Dear,

I recently used Map-splice for my sample. If you have large data set you can simply put a for loop for that. Hope it will help you.

python mapsplice_segments.py -Q fq -w 100 -B bow_tie_build_hg19/hg19 -u test1.fastq -c bow_tie_build_hg19/chr_all/ -o mapsplice_out_test1

[Grouse]

I can get it to run as a loop but no circRNA output is provided.

[archana.bioinfo87]

Just check your read length and other parameters.

[Grouse]

I've tried numerous times. Do you have a copy of the full manual by any chance?

[archana.bioinfo87]

Sorry dear, I am also searching for user manual. I don't have.

Answer 1

[archana.bioinfo87]

Dear,

In your command you missed something here

--fusion --fusion-non-canonical

See the help in Mapsplice2 where it is written like

--fusion |  --fusion-non-canonical

May be this is the reason of your error.

Answer 2

[Grouse]

Awesome! Thanks! I did manage to get MapSplice2 running by removing the --fusion-non-canonical flag even though circRNAs are products of non-canonical splicing.

[Tye Kahn]

Indeed, looks like it is a parameter in whether one or another are chosen, but not both at the same time; as the --fusion-non-canonical parameter already includes the former results (from --fusion). So if in your case you think that actually, the '--fusion-non-canonical' flag is the adequate one, I would recommend removing the '--fusion' instead (should work one way or another).

[Andrea]

Hi! I am having the issue. MapSplice runs but it has 0 circRNA predictions. Can I ask what is the final command you used? Thanks in advance!