User: y.hoogstrate

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y.hoogstrate450
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450
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Netherlands
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1 day, 23 hours ago
Joined:
3 years, 8 months ago
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Posts by y.hoogstrate

<prev • 83 results • page 1 of 9 • next >
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Answer: A: SAM to BAM conversion ERRORS
... SAM consists of 2 parts: - the header (describing which reference genome with corresponding sequences was used as reference and which aligner was used) - the body (alignment relative to the sequences in the header) you seem to have a SAM file that only contains part 2: the body. I don't know whe ...
written 7 days ago by y.hoogstrate450
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Comment: C: Galaxy tool development - how do I get a working samtools?
... Not sure what your exact use-case is, but maybe you could use sambamba as drop-in replacement and revert back to bioconda. Changing the channel order, once it would work, may solve samtools but may break other tools. Since bioconda is supposed to be used as dependency resolver for Galaxy, this would ...
written 5 weeks ago by y.hoogstrate450
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Comment: C: Galaxy tool development - how do I get a working samtools?
... The path of samtools is `/nfs/sw/apps/galaxy-dev/galaxy/database/dependencies/_conda/envs/mulled-v1-ee953de1640e372d8d33733402c4e38671d17286210a6464d4805ae7ef8e67df/bin/samtools` and some of the libraries are in there as well. I think your galaxy and tools are working fine but the bioconda package i ...
written 5 weeks ago by y.hoogstrate450
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Answer: A: Galaxy tool development - how do I get a working samtools?
... ``` samtools ``` should refer to the (i suppose bioconda) version of samtools 1.5 This is the way this should work I believe. Can you run: ```which -a samtools ; ldd `which samtools```` in your tool and post the output? ...
written 5 weeks ago by y.hoogstrate450
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Answer: A: How to make Bowtie2 align a specific number of nt
... ` -3/--trim3 trim bases from 3' (right) end of reads` ...
written 11 weeks ago by y.hoogstrate450
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Comment: C: Issue with Crossmap in local Galaxy instance
... This issue has been resolved in the latest revision of crossmap. Could you confirm this? ...
written 12 weeks ago by y.hoogstrate450
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Comment: C: Issue with Crossmap in local Galaxy instance
... I get the point, thanks. I will take a look at this, I am quite certain this is possible :) ...
written 12 weeks ago by y.hoogstrate450
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Answer: A: Issue with Crossmap in local Galaxy instance
... Hi there (and thanks to Jennifer to bring me here). I knew back then (2015) there were problems with CrossMap (in particular with the installation) and I stopped working on this because I was aware of the upcoming transistion to BioConda. After that transition was completed, I did some updates but ...
written 3 months ago by y.hoogstrate450
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Answer: A: HT-seq counts help
... Mdup most likely refers to http://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates Maybe you can extract the BAM headers. It could be the picard settings are included. ...
written 3 months ago by y.hoogstrate450
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Comment: C: User Tool Does Not Initialize
... Ooops, those comments should be replaced with CDATA tags (blame me!): ``` $output/file.txt ]]> ``` "After I fixed that, the program doesn't hang anymore, but it just doesn't start now." Does the whole Galaxy wrapper not load, or does the command not get executed? *This program is a wrapper fo ...
written 6 months ago by y.hoogstrate450

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Scholar 14 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
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Scholar 23 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
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