User: bimbam42

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bimbam4210
Reputation:
10
Status:
New User
Location:
Switzerland
Last seen:
3 years, 7 months ago
Joined:
3 years, 12 months ago
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b*******@gmail.com

Posts by bimbam42

<prev • 12 results • page 1 of 2 • next >
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Comment: C: GTF usage in Cufflinks
... Hi Jen, I solved the problem. I found out that it is easier to use a gff file that I modify before using it with cufflinks. Cufflinks uses a script to convert gff to gtf: gffread -E annotation.gff -T -o- | more My idea war to have EntrezGeneIds instead of GFF ID=genexxx. Thanks for replaying an ...
written 3.6 years ago by bimbam4210
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GTF usage in Cufflinks
... My problem is that Cufflinks does not recognize the gtf file that I provide. It shows an error that the gff ID is duplicated but I am not using a gff file. How can I set the parameter as gtf so that Cufflinks will use my gtf file?   ...
cufflinks gff_ids reference annotation written 3.7 years ago by bimbam4210 • updated 3.2 years ago by archana bhardwaj20
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Comment: C: SpeedUp Tophat2 (segment_juncs only runs single core)
... Thanks, I map against the bosTau6 (cow) and I also have a gff annotation file as reference. I also printed the command I'm using. Maybe you see setting that can lead to major speed up. My fastq file contains 27690231 sequences, which is pretty big. Here is the command I used: tophat2 --num-threa ...
written 3.9 years ago by bimbam4210
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SpeedUp Tophat2 (segment_juncs only runs single core)
... Is there a possibility to speed up tophat2? My Tophat2 runs with 8 Cores but after a while of computing segment_juncs runs on single core and takes more than 24 hours. Is there anything that I can change in my setting to speed up this process?   ...
tophat written 3.9 years ago by bimbam4210 • updated 3.9 years ago by Jennifer Hillman Jackson25k
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Comment: C: Problems adding bulid-in genomes for tophat on local galaxy
... I solved the problem. My tophat2.xml file pointed to a wrong index file name. But thanks for your help. ...
written 4.0 years ago by bimbam4210
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Answer: A: Problems adding bulid-in genomes for tophat on local galaxy
... Has anyone more hints after having a look at my xml files? Or is there anything else I could try? ...
written 4.0 years ago by bimbam4210
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Comment: C: Problems adding bulid-in genomes for tophat on local galaxy
... Thanks for you hints: My View Data Tables Registry look good. Same for the tool_data_table_conf.xml file. only the bwa index files are missing https://www.dropbox.com/s/qeu8ej7fyimoqlx/shed_tool_data_table_conf.xml https://www.dropbox.com/s/1nn94frhspf2ay2/tool_data_table_conf.xml bowtie ...
written 4.0 years ago by bimbam4210
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Comment: C: Problems adding bulid-in genomes for tophat on local galaxy
... https://www.dropbox.com/s/h5jp7svizv9kwdz/bowtie2_indices.loc ...
written 4.0 years ago by bimbam4210
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Comment: C: Problems adding bulid-in genomes for tophat on local galaxy
... it looks like this: https://www.dropbox.com/s/yevmjp8ix3cks28/tophat2.png   ...
written 4.0 years ago by bimbam4210
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Answer: A: Problems adding bulid-in genomes for tophat on local galaxy
... Hello again. I still have no luck with the build-in genomes for tophat2. My files have real TABs and they are accessible for my galaxy user. The first column and the dbkey are the same like in  tool-data/shared/ucsc/build.txt. Or do I need to change the build.txt somewhere else? I also see my chan ...
written 4.0 years ago by bimbam4210

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