User: GokalpC

gravatar for GokalpC
GokalpC50
Reputation:
50
Status:
New User
Location:
Turkey/Ankara/Intergen
Last seen:
2 days, 4 hours ago
Joined:
1 year, 1 month ago
Email:
g******************@gmail.com

Posts by GokalpC

<prev • 13 results • page 1 of 2 • next >
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Answer: A: How to concatenate four fastq files of NextSeq in linux?
... It is better not to merge/cat fastq data from different lanes. Just start processing them as individual until duplicate marking stage or another where you can merge bam files with different read group names. ...
written 26 days ago by GokalpC50
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Answer: A: merge VCF single variants G>A and C>A into GC>AA
... If they are in phase then ReadBackedPhasing will set them together but that is an old tool from GATK3 era. Another useful strategy is to enable MNP calling with your variant caller. Freebayes does this by default or GATK4 HC can be adjusted to call MNPs with given distance. Other than the read i ...
written 26 days ago by GokalpC50
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Answer: A: What does it mean if a gene is not found in an assembly?
... I would suggest mapping reads to transcriptomes to see if the gene of interest has at least some degree of presence among the reads. It is quite likely that you will find something that may resemble the gene (albeit with low homology) that you are searching for. ...
written 9 months ago by GokalpC50
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Comment: C: variant calling - data from IonTorrent technology
... You may want to check the docker hub from iontorrent https://hub.docker.com/u/iontorrent They have the latest software in containers and ready to use. You don't need to have access to a seperate server if you have plenty of desktop horsepower for this. Their documentation is also good. ...
written 9 months ago by GokalpC50
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Comment: C: how to fix the error - Too many open files - by changing code in python3.7
... You are right. However file write is not done through fo.write() or fu.write() routines. Maybe print statement is not checking the fu and fo being opened as one file but tries to open and write at each time this for loop proceeds. I would suggest write file lines to be modified like the ones given i ...
written 10 months ago by GokalpC50
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Comment: C: how to fix the error - Too many open files - by changing code in python3.7
... Agreed however some algorithms or even some old software or software coded by 3rd party requires these adjustments for proper functioning. There is really nothing to do but modify system settings in those cases. One thing that I noticed is that file ops do not close the buffers therefore those ope ...
written 10 months ago by GokalpC50
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Answer: A: some unrelated info in SAM file generated by BWA
... If you must use nohup and there is no -o FILE option call bwa from an inner bash call. nohup bash -c 'bwa mem -t 12 GRCh38.bwa VEGFA_site_1.fastq.gz > VEGFA_site_1_output.sam' & That should take care improper redirection of stdout. ...
written 10 months ago by GokalpC50
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Answer: A: how to fix the error - Too many open files - by changing code in python3.7
... You need to increase the open file limit from /etc/security/limits.conf If your distro is systemd based sometimes there are other files to edit to get there such as /etc/systemd/system.conf ...
written 10 months ago by GokalpC50
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Answer: A: bcl2fastq on Mac
... Why don't you try docker for mac. You can try various images under docker hub. I recently released a compatible build with many kernel versions. docker pull skysbiodocker/bcl2fastq2 ...
written 10 months ago by GokalpC50
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Answer: A: Issues installing bcl2fastq?
... Hi Sorry that this is a very late reply for a repository for this build. Finally I generated a docker image for this build. It can be had from skysbiodocker/bcl2fastq2 docker pull skysbiodocker/bcl2fastq2 There is another docker image that I used to use which is the illumina rpm build base ...
written 10 months ago by GokalpC50

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