User: thomasvangurp

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Posts by thomasvangurp

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Job: Python developer genomics software | near Amsterdam, The Netherlands
... **Python Developer** For 32-40 hours per week. Apply before: 29th of may 2018 **What would you do?** For our bioinformatics team we are looking for a Python Developer for 36-40 hours per week in Roelofarendsveen (near Amsterdam, the Netherlands) In this role, you have the opportunity to write ...
python computer science cs bioinformatics job written 5 months ago by thomasvangurp0
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Faster version of RPS-BLAST (Reverse PSI-BLAST) USearch/Vsearch
... I am using NCBI's RPS-blast for finding conserved domains in protein sequence data. Given that usearch/vsearch/diamond are orders of magnitude faster than NCBI's blast (although with somewhat lower accuracy), I was wondering if anyone knows if a faster implementation of RPS-blast exists. With kind ...
usearch blast vsearch written 18 months ago by thomasvangurp0 • updated 18 months ago by h.mon20k
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Comment: C: Piping With Samtools, Bwa And Bedtools
... Hi Ying, I was trying to follow the workflow described above but could not get it to work using bwa-mem.. Have you found a way to do this? samtools view complains about truncated input. ...
written 4.9 years ago by thomasvangurp0
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Comment: C: Per Sample Mpileup Output From Merged Bam File
... Thanks A lot for posting this here Ying, sorry for crossposting. I still think it's useful as samtools-help is not as easily searchable as biostars. ...
written 4.9 years ago by thomasvangurp0
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Comment: C: Per Sample Mpileup Output From Merged Bam File
... Thanks, I thought that the SM tag in in the @RG header was meant to achieve calling variants from a single file. From http://samtools.sourceforge.net/mpileup.shtml : "SAMtools acquires sample information from the SM tag in the @RG header lines. One alignment file can contain multiple samples; reads ...
written 4.9 years ago by thomasvangurp0
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Per Sample Mpileup Output From Merged Bam File
... I'd like to run mpileup on a bam file with two different samples. The samples are identified in the header in the following way: @RG ID:ApeKI_s2.sort SM:ApeKI_s2.sort LB:citrus_ApeKI PL:ILLUMINA @RG ID:ApeKI_s12.sort SM:ApeKI_s12.sort LB:citrus_ApeKI PL:ILLUMINA I added th ...
samtools mpileup written 4.9 years ago by thomasvangurp0 • updated 4.9 years ago by Ying W3.8k
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Job: Experienced Bioinformatician - Netherlands Institute Of Ecology
... Bioinformatician (embedded) Sequencing is becoming a major technique in ecology and in the life sciences in general. The second and third generation sequencing platforms produce more data and the cost per base pair are going down. This enables more and more researchers to have their samples sequence ...
next-gen python job hardware bioinformatician illumina written 5.3 years ago by thomasvangurp0 • updated 5.3 years ago by Eric Normandeau9.9k

Latest awards to thomasvangurp

Popular Question 3.0 years ago, created a question with more than 1,000 views. For Experienced Bioinformatician - Netherlands Institute Of Ecology
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Per Sample Mpileup Output From Merged Bam File

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