User: dfajar2

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dfajar290
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Posts by dfajar2

<prev • 12 results • page 1 of 2 • next >
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Comment: C: bcftools DP filtering and recode as vcftools, but for polyploids?
... Thanks!! I didn't knew about the plugins!!! It worked great. ...
written 6 months ago by dfajar290
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bcftools DP filtering and recode as vcftools, but for polyploids?
... Hi, I use Freebayes as variant caller and I usually use vcftools to perform hard filtering of variants based on minimum depth values. So for example, if any sample has a value of less than 8 reads (DP), the GT is not taken into account. An example of the output (after using vcf-query) is: S ...
vcf vcfools bcftools snp written 7 months ago by dfajar290
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Comment: C: How to break script if Bowtie2 errors?
... Well, I learned something new today. Thx ...
written 12 months ago by dfajar290
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Comment: C: How to break script if Bowtie2 errors?
... Perfect, thanks!!!! I tried set -e in the past and that didn't work. :-) ...
written 12 months ago by dfajar290
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How to break script if Bowtie2 errors?
... Hi, I'll try to explain my problem the best I can. I have a script that runs multiple bowtie2 alignments. The problem is that it continues running the next alignment even if the current one fails to run. **script.sh** #!/bin/bash bowtie2 --threads 32 -x sp_idx -U reads1.fastq | samtools ...
bowtie2 written 12 months ago by dfajar290
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Answer: A: Error installing bcl2fastq 2.20 in make step - Ubuntu 18.04
... I finally found a post on how to install bcl2fastq v2.20 from a tarball. I followed the instructions and installed it with no errors!!! https://sarahpenir.github.io/linux/Installing-bcl2fastq/ ...
written 13 months ago by dfajar290
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Comment: C: Error installing bcl2fastq 2.20 in make step - Ubuntu 18.04
... I found a solution. Look below ...
written 13 months ago by dfajar290
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Comment: C: Error installing bcl2fastq 2.20 in make step - Ubuntu 18.04
... Well, I'm `glad` I'm not the only one :-) ...
written 13 months ago by dfajar290
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Comment: A: Error installing bcl2fastq 2.20 in make step - Ubuntu 18.04
... Thanks everyone for their suggestions. I am looking to install version 2.20 rather to 2.19. I'll try the rpm approach and also the patch to see if that solves my problem. Thanks I appreciate your help :-) ...
written 14 months ago by dfajar290
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Error installing bcl2fastq 2.20 in make step - Ubuntu 18.04
... After spending numerous hours trying to install bcl2fastq 2.20 in my server I decided to ask for help. I am trying to install bcl2fastq 2.20 in Ubuntu 18.04. I have followed multiple recommendations for fixing inconveniences while installing bcl2fastq with newer boost versions (as in these posts ...
software error ubuntu bcl2fastq written 15 months ago by dfajar290

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Scholar 13 months ago, created an answer that has been accepted. For A: Error installing bcl2fastq 2.20 in make step - Ubuntu 18.04

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