User: opplatek

gravatar for opplatek
opplatek30
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30
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New User
Location:
Czech Republic
Last seen:
3 weeks, 5 days ago
Joined:
4 years, 4 months ago
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Posts by opplatek

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Automating Gorilla And/Or Revigo Analysis
... Thanks for the script! Save me a lot of manual work. Here are few modifications of a couple of lines which I believe are not correct. I am not a Perl guy but it seems it's working better after the changes. **Line 80** should be $mech->set_fields("background_file_name" => $background); ...
written 11 months ago by opplatek30
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Answer: A: Parsing augustus output
... I know it's quite late but in case somebody else has the same question. Augustus has a bunch of scripts for the postprocessing in the installation directory under `augustus-x.x.x/scripts/`. The basic parsing script is called `getAnnoFasta.pl` and takes the resulting gtf/gff as the input and outputs ...
written 11 months ago by opplatek30
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Answer: A: Remove Soft Clipped Bases
... **[bamutils / removeclipping][1]** works also very nice P.S. I know the post is very old but this might be handy for somebody else reading this post in the future. [1]: http://ngsutils.org/modules/bamutils/removeclipping/ ...
written 17 months ago by opplatek30
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Comment: C: Filtering nth length from mapped SAM/BAM file.
... Dear Pierre, I have tried your tool to filter mappings with a minimal mapped length. I see that your filtering is based on the mapped length measured on the reference. I have encountered mapping with CIGAR looking like this `106S8M1D21M14S`. Based on your command the mapping does not get filtered ...
written 2.2 years ago by opplatek30
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Comment: C: Picard CollectRnaSeqMetrics error
... You are missing the gene name at the first column. Check solinvicta comment to fix this. Basically you have to run `gtfToGenePred -genePredExt` and then move the gene name (column 12) to the first column. ...
written 2.5 years ago by opplatek30
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Comment: C: miRDeep2.0.0.8 install error occured
... Thanks, this worked for me. I installed all dependencies and then ran `perl install.pl` in mirdeep2 folder. It gave me an error during ViennaRNA installation. I checked created bin directory in mirdeep2 folder and I saw a soft-link for RNAfold package pointing to "newly" installed RNAfold by `instal ...
written 2.5 years ago by opplatek30
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Answer: A: Suggest Pirna Ngs Small Rna Analysis Pipelines/Workflows
... You can also try Kraken which has a specific part of pipeline just for piRNA analysis (see examples) http://www.ebi.ac.uk/research/enright/software/kraken ...
written 3.0 years ago by opplatek30
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Answer: A: Blat Clumptohsprange Error
... Thanks for this information. I had similar problem but in my case I just received core dumped without any further explanation. Cutting the database into 4GB pieces did the trick. ...
written 4.3 years ago by opplatek30

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