tophat-fusion-post
Hi Emilie,
Thanks a lot for your answer. Was your initial alignment call something like
/packages/tophat/2.0.4/bin/tophat -p 64 -o tophat/tophat_MCF7_final2 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search -r 0 --mate-std-dev 80 --fusion-min-dist 100000 --fusion-anchor-length 13 --fusion-ignore-chromosomes chrM index/hg19 SRR064286_1.fastq SRR064286_2.fastq
for your MCF7 run?
how many fusions did you get?
I'm still getting nothing!
tophat-fusion-post -p 1 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 indexes/hg19
[Wed Oct 3 10:53:02 2012] Beginning TopHat-Fusion post-processing run (v2.0.3)
-----------------------------------------------
[Wed Oct 3 10:53:02 2012] Extracting 23-mer around fusions and mapping them using Bowtie
samples updated
[Wed Oct 3 10:53:24 2012] Filtering fusions
Processing: tophat_MCF7_final2/fusions.out
0 fusions are output in ./tophatfusion_out/potential_fusion.txt
[Wed Oct 3 10:53:32 2012] Blasting 50-mers around fusions
[Wed Oct 3 10:53:32 2012] Generating read distributions around fusions
[Wed Oct 3 10:53:32 2012] Reporting final fusion candidates in html format
num of fusions: 0
-----------------------------------------------
[Wed Oct 3 10:53:33 2012] Run complete [00:00:30 elapsed]
Hi Emilie,
Thanks a lot for your answer. Was your initial alignment call something like
/packages/tophat/2.0.4/bin/tophat -p 64 -o tophat/tophat_MCF7_final2 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search -r 0 --mate-std-dev 80 --fusion-min-dist 100000 --fusion-anchor-length 13 --fusion-ignore-chromosomes chrM index/hg19 SRR064286_1.fastq SRR064286_2.fastq
for your MCF7 run?
how many fusions did you get?
I'm still getting nothing!
tophat-fusion-post -p 1 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 indexes/hg19
[Wed Oct 3 10:53:02 2012] Beginning TopHat-Fusion post-processing run (v2.0.3)
-----------------------------------------------
[Wed Oct 3 10:53:02 2012] Extracting 23-mer around fusions and mapping them using Bowtie
samples updated
[Wed Oct 3 10:53:24 2012] Filtering fusions
Processing: tophat_MCF7_final2/fusions.out
0 fusions are output in ./tophatfusion_out/potential_fusion.txt
[Wed Oct 3 10:53:32 2012] Blasting 50-mers around fusions
[Wed Oct 3 10:53:32 2012] Generating read distributions around fusions
[Wed Oct 3 10:53:32 2012] Reporting final fusion candidates in html format
num of fusions: 0
-----------------------------------------------
[Wed Oct 3 10:53:33 2012] Run complete [00:00:30 elapsed]
Originally posted by Emilie
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