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Old 08-13-2012, 05:40 PM   #1
NKAkers
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Location: New York, NY

Join Date: Sep 2011
Posts: 26
Default Merging tophat2 outputs for tophat-fusion

Hello Tophat users,

I'm having some trouble getting tophat-fusion-post to work with my data. Running a full lane of RNA-seq data resulted in failures at the joining segments step, so I ran each lane split in two, (ie sample1.1 and sample1.2) This worked well, but now I have two unique outputs for every 1 sample.

I attempted to cat together fusions.out from both outputs in a new directory (sample1.3) and then do a sort using the command below:

Code:
cat fusions.out | tr "-" "\t" | sed 's/chr/chr /g' | sort -n -b -k 2 -k 4 -k 5 -k 6 | sed 's/chr /chr/g' | sed 's/\t/-/' > fusions.out1 ; cp fusions.out1 fusions.out
This seems to work, except it puts X and Y ahead of 1 which I didn't think would be a problem. However, when I run tophat-fusion-post I get an error message:

Code:
tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 /bowtie/bowtie-0.12.8/hg19/hg19


[Mon Aug 13 16:41:08 2012] Beginning TopHat-Fusion post-processing run (v2.0.3)
-----------------------------------------------
[Mon Aug 13 16:41:08 2012] Extracting 23-mer around fusions and mapping them using Bowtie
        samples updated

Mon Aug 13 17:07:46 2012] Filtering fusions
        Processing: tophat_sample01.1/fusions.out
        Processing: tophat_sample01.2/fusions.out
        Processing: tophat_sample01.3/fusions.out
Traceback (most recent call last):
  File "/tophat2/tophat-2.0.3.Linux_x86_64/tophat-fusion-post", line 2083, in <module>
    sys.exit(main())
  File "/tophat2/tophat-2.0.3.Linux_x86_64/tophat-fusion-post", line 2054, in main
    filter_fusion(bwt_idx_prefix, params)
  File "/tophat2/tophat-2.0.3.Linux_x86_64/tophat-fusion-post", line 695, in filter_fusion
    filter_fusion_impl(fusion_file, refGene_list, ensGene_list, seq_chr_dic, fusion_gene_list)
  File "/tophat2/tophat-2.0.3.Linux_x86_64/tophat-fusion-post", line 488, in filter_fusion_impl
    if abs(int(left)) + abs(int(right)) > 2000:
ValueError: invalid literal for int() with base 10: ''
Has anyone had to merge separated tophat outputs? Any ideas why I'm getting this error? Does tophat-fusion-post rely on any files besides fusions.out?

Thanks in advance.
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Old 08-15-2012, 06:40 PM   #2
NKAkers
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Location: New York, NY

Join Date: Sep 2011
Posts: 26
Default

Sorry folks, this was just a dumb error on my part. I was inadvertently changing fusions.out when I sorted it. Here is better code for sorting, if anyone wants it.

Code:
cat fusions.out | sed 's/-/\t/' | sed 's/chr/chr /g' | sort -n -b -k 2 -k 4 -k 5 -k 6 | sed 's/chr /chr/g' | sed 's/\t/-/' > fusions.out1 ; cp fusions.out1 fusions.out ; rm fusions.out1
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