User: y.hoogstrate

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y.hoogstrate460
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Netherlands
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1 month ago
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4 years, 1 month ago
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Posts by y.hoogstrate

<prev • 84 results • page 1 of 9 • next >
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Answer: A: Want all counts on MPileup including zero counts
... The arguments `-a` and `-aa` have not yet been implemented in the galaxy wrapper. This feature is BTW only available in the latest samtools version as samtools 1.3.1 does not even have it (but 1.6 does). ...
written 4 months ago by y.hoogstrate460
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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 5 months ago by y.hoogstrate460
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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 6 months ago by y.hoogstrate460
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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 6 months ago by y.hoogstrate460
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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 6 months ago by y.hoogstrate460
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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 7 months ago by y.hoogstrate460
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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 7 months ago by y.hoogstrate460
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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 8 months ago by y.hoogstrate460
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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 8 months ago by y.hoogstrate460
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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 8 months ago by y.hoogstrate460

Latest awards to y.hoogstrate

Great Question 3 months ago, created a question with more than 5,000 views. For Making PNG figures from plots in R from toolshed (without X11)
Scholar 19 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Scholar 20 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Scholar 20 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Scholar 20 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
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Scholar 2.3 years ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Scholar 2.3 years ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Is HISAT2 working in GALAXY?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Making PNG figures from plots in R from toolshed (without X11)

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