User: colindaven
colindaven • 1.8k
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Posts by colindaven
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Answer:
A: Variant using freebayes
... Sounds challenging. Is it really 4n or a double haploid (would be a lot easier).
This thread might be helpful
https://www.biostars.org/p/94068/
Make sure you look at your results in a genome browser. Certainly a few read errors in the sequencing might be difficult to discern from the type of var ...
written 3 hours ago by
colindaven • 1.8k
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... Have a look at bedtools intersect for this, there are great docs and tutorials there.
http://quinlanlab.org/tutorials/bedtools/bedtools.html ...
written 2 days ago by
colindaven • 1.8k
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... We have extended the deadline on this position. If you are interested in seeing established big data approaches brought closer to the clinic please apply. German language skills are a distinct advantage. ...
written 8 days ago by
colindaven • 1.8k
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... You might be able to repair this using **repair.sh** from the bbmap package (install via bioconda if you like).
By repair I mean get R1 and R2 files of the same length with the corresponding reads and headers.
eg
repair.sh -Xmx40g in=A1_03_S2_2_R1.fastq in2=A1_03_S2_2_R2.fastq out1=A1_03_S2_ ...
written 10 days ago by
colindaven • 1.8k
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... Could it be that it is swapping ? Eg install htop and/or glances if on ubuntu and check the hard disk is not being used and RAM is not full.
How much RAM do you have ? ...
written 10 days ago by
colindaven • 1.8k
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... Short reads are definitely still required. Else artificial frameshifts can be found everywhere. ...
written 11 days ago by
colindaven • 1.8k
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Answer:
A: snpEff Apis_mellifera genome
... Do you have a proxy ?
You might be able to get it to work by putting this in your .bashrc and logging out and back in.
Obviously edit
MYPROXYIPADDRESS
and
port 8080
to your institutions's details.
_JAVA_OPTIONS=-Dhttp.proxyHost=MYPROXYIPADDRESS -Dhttp.proxyPort=8080 -Dhttps.proxyHost=MYPRO ...
written 17 days ago by
colindaven • 1.8k
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... Acceptance still pretty low in my estimation. We have a CPU cluster and no GPUs, but we are working towards getting a GPU.
For image analysis and neural nets GPUs are great of course. If I were you I'd definitely get the workstation. ...
written 23 days ago by
colindaven • 1.8k
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Comment:
C: Allelic-Specific RNA-Seq pipeline
... He/we already recommended phaser a couple of times. It is not an easy task, so good luck! The mouse genome is not phased. Illumina even made a video about this: https://www.youtube.com/watch?v=15NPZCGP_e4 ...
written 23 days ago by
colindaven • 1.8k
3
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... There are a few GPU projects, eg here https://developer.nvidia.com/Clara-Genomics
(interestingly minimap2 is getting the gpu treatment)
and there have been a few in the past, eg. soap3-dp, bwagpu, some accelerated GPU blast-like programs, etc, but in general there hasn't been great uptake in the c ...
written 23 days ago by
colindaven • 1.8k
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