Question: Protein Domains from fusions
0
gravatar for Ron
3.6 years ago by
Ron960
United States
Ron960 wrote:

Hi all,

I came across this post on finding protein domains from gene fusions,so used this software "Oncofuse".

A: Oncofuse: Prediction Of Driver Gene Fusions From Ngs Data

My input is the STAR-fusion output.My command is following which runs,but the output from Oncofuse is an empty file.

java -Xmx1G -jar $onco_dir/Oncofuse.jar $fusionresults_dir/star-fusion.fusion_candidates.final.abridged starfusion AVG  $onco_dir/out_onco.txt

 

Log file is below:

 more oncofuse.sh.o515938.1 

Dec 22, 2015 12:20:12 PM org.codehaus.groovy.runtime.m12n.MetaInfExtensionModule newModule

WARNING: Module [groovy-all] - Unable to load extension class [org.codehaus.groovy.runtime.NioGroovyMethods]

[Tue Dec 22 12:20:13 EST 2015] Loading RefSeq data, assuming hg19

[Tue Dec 22 12:20:13 EST 2015] Reading input file, assuming STARFUSION format

Ignoring line #fusion_name    JunctionReads    SpanningFrags    Splice_type    LeftGene    LeftBreakpoint    RightGene    RightBreakpoint

Ignoring line NCOA4--RET    57    35    ONLY_REF_SPLICE    NCOA4^ENSG00000138293.15    chr10:51582939:+    RET^ENSG00000165731.13    chr10:43612032:+

Ignoring line DHRS3--CCDC27    28    14    ONLY_REF_SPLICE    DHRS3^ENSG00000162496.4    chr1:12638746:-    CCDC27^ENSG00000162592.4    chr1:3683099:+

Ignoring line RET--NCOA4    9    6    ONLY_REF_SPLICE    RET^ENSG00000165731.13    chr10:43610184:+    NCOA4^ENSG00000138293.15    chr10:51584616:+

Ignoring line RP11-680G10.1--GSE1    4    2    ONLY_REF_SPLICE    RP11-680G10.1^ENSG00000261567.1    chr16:85391249:+    GSE1^ENSG00000131149.13    chr16:85682158:+

Ignoring line RP11-680G10.1--GSE1    1    2    ONLY_REF_SPLICE    RP11-680G10.1^ENSG00000261567.1    chr16:85391249:+    GSE1^ENSG00000131149.13    chr16:85667520:+

[WARNING] No valid fusions in input file!

[Tue Dec 22 12:20:13 EST 2015] Mapping breakpoints to known genes (this is going to filter a lot)

[Tue Dec 22 12:20:13 EST 2015] 0 fusions mapped out of 0. Dropped fusion candidates: 0 - 5'FPG not mapped, 0 - 3'FPG not mapped, 0 - mapped to same gene, 0 - discordant FPG directions

[Tue Dec 22 12:20:13 EST 2015] Getting features for FPG parts

[Tue Dec 22 12:20:13 EST 2015] Loading expression-related data

[Tue Dec 22 12:20:14 EST 2015] Loading domain and protein interaction interface-related data

[Tue Dec 22 12:20:15 EST 2015] Loading gene ontology data (time-consuming)

[Tue Dec 22 12:20:17 EST 2015] Annotating FPG parts

[Tue Dec 22 12:20:17 EST 2015] =Stage #1: raw data

[Tue Dec 22 12:20:17 EST 2015] ==Domain & PII related

[Tue Dec 22 12:20:17 EST 2015] ==Tissue specific

[Tue Dec 22 12:20:17 EST 2015] =Stage #2: some computations

[Tue Dec 22 12:20:17 EST 2015] ==Domain & PII related (time-consuming)

[Tue Dec 22 12:20:17 EST 2015] ==Tissue specific

[Tue Dec 22 12:20:17 EST 2015] Initializing classifier

[Tue Dec 22 12:20:17 EST 2015] Classifying fusions

[Tue Dec 22 12:20:17 EST 2015] Writing output

 

Let me know if any suggestions regarding using this software.

Thanks,

Ron

rna-seq next-gen fusion domain • 1.3k views
ADD COMMENTlink modified 3.6 years ago by mikhail.shugay3.3k • written 3.6 years ago by Ron960
0
gravatar for mikhail.shugay
3.6 years ago by
mikhail.shugay3.3k
Czech Republic, Brno, CEITEC
mikhail.shugay3.3k wrote:

Hello! You can try to remove the Splice_type column from the input and run it again. Let me know if it helps. Also check if it runs on https://github.com/mikessh/oncofuse/blob/legacy/src/main/resources/example/example_starfusion.txt file to rule.

ADD COMMENTlink written 3.6 years ago by mikhail.shugay3.3k

Hi,

I removed the Splice type column,it does not work.But the example file you mentioned gives results.It has extra columns 

LeftDistFromRefExonSplice,

 
RightDistFromRefExonSplice

probably because of that?

ADD REPLYlink written 3.6 years ago by Ron960

Yes, it appears that the example file was from older version/format. Changing the columns so that they are the same as in example file should work.

ADD REPLYlink written 3.6 years ago by mikhail.shugay3.3k

So I would add two columns with 0's.Hope it does not impact the results.

ADD REPLYlink written 3.6 years ago by Ron960

I added the 2 columns to get the output.Can we get any graphical output?

ADD REPLYlink written 3.6 years ago by Ron960
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