User: alhamidi.reem

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Posts by alhamidi.reem

<prev • 12 results • page 1 of 2 • next >
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Comment: A: Struggling to use the GATK HaplotypeCaller on my bam files.
... Thank you all for your responses. I appreciate it. ...
written 16 days ago by alhamidi.reem10
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Comment: C: GATK -Xmx4G and -Xmx8G
... Thanks alot, Andrew. ...
written 16 days ago by alhamidi.reem10
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GATK -Xmx4G and -Xmx8G
... Dear all, I would like to know what the difference is between the "-Xmx4G" and "-Xmx8G" switches on GATK. All I know is, both of these switches are used for specifying memory allocation (which I'm still not quite sure I understand the meaning of it) from https://software.broadinstitute.org/gatk/doc ...
haplotypecaller gatk bioinformatics written 16 days ago by alhamidi.reem10 • updated 16 days ago by andrew.j.skelton735.8k
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Struggling to use the GATK HaplotypeCaller on my bam files.
... Good morning everyone, I have downloaded the current version on my linux server from https://software.broadinstitute.org/gatk/download/ using the following command: $ wget "https://github.com/broadinstitute/gatk/releases/download/4.1.2.0/gatk-4.1.2.0.zip" The software was download and the jar ...
haplotypecaller gatk software error written 21 days ago by alhamidi.reem10
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How to extract the first and last N bases from a read in a fastq file?
... how can I extract the first and last N bases from a read in a fastq file? I have used the following command to extract the last 1000 bases of a read from a fastq file but I'd also like to incorportate the first 1000 bases to the command as well: $$ grep -A 4 "read_name_identifier" filename.fq ...
bioinformatics written 12 weeks ago by alhamidi.reem10 • updated 12 weeks ago by genomax69k
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Comment: C: Extracting last N bases of reads in FASTQ file
... Hi @genomax, thank you for your reply. but I have just modified my question, I meant how I could extract the first and last N bases from a read in a fastq file? I have used the following command to extract the last 1000 bases of a read from a fastq file but I'd like to incorportate the first 1000 b ...
written 12 weeks ago by alhamidi.reem10
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Comment: C: Extracting last N bases of reads in FASTQ file
... Hi @pld, thanks for sharing this. What would be used if I wanted to exrtact the first and last 5 bases of a fastq file? What should be typed in differently for the second line after the pipeline? ...
written 3 months ago by alhamidi.reem10
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Comment: C: How Can I Know The Length Of Mapped Reads From Bam File?
... Hi Zev, what would the syntax be if I include indels and gaps in the reads? Many thanks, Reem Alhamidi ...
written 3 months ago by alhamidi.reem10
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Comment: A: Definition of minor and major allele and connection with risk, effect, wildtype
... Thank you Kevin for your explanations :) ...
written 3 months ago by alhamidi.reem10
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Comment: C: Understanding Conditional analysis
... Hi Veera, the link/page is not found. Can you share the recent/up to date link please? ...
written 4 months ago by alhamidi.reem10

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