User: julianneradford

Reputation:
0
Status:
New User
Last seen:
1 week, 2 days ago
Joined:
2 months, 3 weeks ago
Email:
j**************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by julianneradford

<prev • 11 results • page 1 of 2 • next >
0
votes
0
answers
52
views
0
answers
How can I analyze a VCF dataset without an annotated reference genome
... 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 ...
genome R galaxy rna-seq gatk written 10 days ago by julianneradford0
0
votes
0
answers
125
views
0
answers
Comment: C: Mapping transcriptomes against each other to find genetic differences
... 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 julianneradford0
0
votes
1
answer
86
views
1
answers
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 julianneradford0
0
votes
1
answer
86
views
1
answers
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 julianneradford0
0
votes
1
answer
86
views
1
answers
Comment: 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 julianneradford0
2
votes
1
answer
86
views
1
answer
Samtools command not found
... 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 ...
error written 13 days ago by julianneradford0
0
votes
1
answer
163
views
1
answers
Comment: C: Checking ReadGroup name in BAM file error: E26: Hebrew cannot be used: Not enabl
... 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 julianneradford0
0
votes
1
answer
163
views
1
answers
Comment: C: Checking ReadGroup name in BAM file error: E26: Hebrew cannot be used: Not enabl
... 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 julianneradford0
1
vote
1
answer
163
views
1
answer
Checking ReadGroup name in BAM file error: E26: Hebrew cannot be used: Not enabled at compile time
... 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 \ ...
gatk rna-seq written 16 days ago by julianneradford0 • updated 16 days ago by Pierre Lindenbaum134k
1
vote
1
answer
104
views
1
answer
GATK HaplotypeCaller Error
... 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 \ ...
haplotypecaller gatk java rna-seq error written 25 days ago by julianneradford0 • updated 25 days ago by Pierre Lindenbaum134k

Latest awards to julianneradford

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2234 users visited in the last hour
_