User: julianneradford
julianneradford • 0
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Posts by julianneradford
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... Hi there,
I am trying to compare genomic variation across 8 transcriptome libraries. I have cleaned up the data, mapped it with BWA, marked duplicates, sorted the BAM, used FreeBayes to make the VCF files. However, I do not have an annotated reference genome for the species (Reticulitermes flavipe ...
written 10 days ago by
julianneradford • 0
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... I have a list of genes that I want to compare as opposed to doing the genome-wide analysis. Is it possible to compare them without an annotation? If so, do you have any ideas on what tools I can use to do this?
Thanks. ...
written 10 days ago by
julianneradford • 0
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Comment:
C: Samtools command not found
... Thank you so much for the help! I ended up editing the .bashrc and adding samtools to the path that way, and that worked!!! Working fine now. ...
written 11 days ago by
julianneradford • 0
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Comment:
C: Samtools command not found
... Thanks for the replies. Even when I use the same shell, I get the same error. Any other ideas? Thanks. ...
written 12 days ago by
julianneradford • 0
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C: Samtools command not found
... yes I did do that I just didn't bother to put it in the post haha thx. ...
written 12 days ago by
julianneradford • 0
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... Hi there!
I installed samtools according to the instructions from here: https://gatk.broadinstitute.org/hc/en-us/articles/360041320571--How-to-Install-all-software-packages-required-to-follow-the-GATK-Best-Practices
I downloaded the samtools tar file version 1.11.
Unpacked it with:
tar xvj ...
written 13 days ago by
julianneradford • 0
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... Okay I see. I checked that and it says for all of the directories I've added "no such file or directory" Clearly I must not be adding things to my PATH correctly then. I have been added the following directories to my PATH in this way:
export PATH="$/Applications/Python\ 2.7/:$PATH"
export ...
written 16 days ago by
julianneradford • 0
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... Hello! Thanks for your reply. However, when I use
samtools view
I get this error:
samtools: command not found
I (think) I have followed all instructions to properly install samtools, add it to the path, and am making sure I am working in the right directory so I am not sure why this hap ...
written 16 days ago by
julianneradford • 0
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... Hi there!
My ultimate goal is to run GATK4.1.9.0 HaplotypeCaller on some BAM files. I used this code:
(base) Juliannes-MacBook-Pro:gatk-4.1.9.0 julianneradford$ ./gatk HaplotypeCaller \
> -R Rflav_transcriptome_sequences.fa \
> -I SRR5341585.bam \
> -O 85variants.g.vcf \ ...
written 16 days ago by
julianneradford • 0
• updated
16 days ago by
Pierre Lindenbaum ♦ 134k
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... Hi there!
Hi there,
I am trying to run GATK's (v 4.1.9.0) HaplotypeCaller using CLI on my Mac to acquire VCFs from some bam files, using this command for the first file:
./gatk HaplotypeCaller \
- R Rflav_transcriptome_sequences.fa \
- I SRR5341585.bam \
- O 85variants.g.vcf \ ...
written 25 days ago by
julianneradford • 0
• updated
25 days ago by
Pierre Lindenbaum ♦ 134k
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