User: opplatek

gravatar for opplatek
opplatek40
Reputation:
40
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New User
Location:
Czech Republic
Last seen:
4 hours ago
Joined:
5 years, 4 months ago
Email:
o*******@gmail.com

Posts by opplatek

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Convert BLAT to GFF file?
... [This][1] works fine. [1]: http://eugenes.org/gmod/tandy/blat2gff.pl ...
written 5 months ago by opplatek40
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Comment: C: How Can I Know The Length Of Mapped Reads From Bam File?
... The `bam2bed` will fail if you have spliced alignments. But he didn't specify if DNA or RNA alignment in the question so the answer is still valid. ...
written 9 months ago by opplatek40
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Comment: C: Remove Soft Clipped Bases
... I have edited the answer and link should be working now. The team stopped actively supporting the tools and they have migrated [here][1]. However, I don't see the clipping utility there. The 'old' one still works, though. The `bamUtil` is completely different package. [1]: https://compgen.io/ng ...
written 9 months ago by opplatek40
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Comment: C: Fastx_toolkit with nanopore data
... You might have to add `qin=33` to the `reformat.sh` making it `reformat.sh qin=33 in=your.fastq out=your.fasta` otherwise you might get `Warning! Changed from ASCII-33 to ASCII-64 on input ;: 59 -> 28`. ...
written 11 months ago by opplatek40
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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 23 months ago by opplatek40
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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 23 months ago by opplatek40
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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]: https://github.com/ngsutils/ngsutils/blob/master/ngsutils/bam/removeclipping.py ...
written 2.5 years ago by opplatek40
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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 3.2 years ago by opplatek40
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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 3.5 years ago by opplatek40
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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 3.5 years ago by opplatek40

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