User: rquigl01

gravatar for rquigl01
rquigl0110
Reputation:
10
Status:
New User
Location:
Last seen:
2 years ago
Joined:
2 years ago
Email:
r*******@rams.shepherd.edu

Posts by rquigl01

<prev • 11 results • page 1 of 2 • next >
0
votes
1
answer
621
views
1
answers
Comment: C: Calling variants help
... mpileup and unified genotyper. Freebayes works but it doesnt open in IGV ...
written 2.0 years ago by rquigl0110
0
votes
1
answer
621
views
1
answers
Comment: C: Calling variants help
... mpileup and unified genotyper. Freebayes works but it doesnt open in IGV ...
written 2.0 years ago by rquigl0110
0
votes
1
answer
621
views
1
answers
Comment: C: Calling variants help
... freebayes doesnt open in IGV. All it says is malformed header ...
written 2.0 years ago by rquigl0110
2
votes
1
answer
621
views
1
answer
Calling variants help
... Hello Galaxy Biostar, For the past three weeks I've been trying to call SNPs and INDELs on my NGS samples for a summer research project. I'm a college student and all of this is new to me, but I've learned so much in these past three weeks. So far I have put my fastq files through bowtie2 on galaxy ...
calling mpileup galaxy snps indels written 2.0 years ago by rquigl0110 • updated 2.0 years ago by bryantl90
0
votes
2
answers
1.0k
views
2
answers
Answer: A: Cannot set metadata on .bcf output from mpileup
... I had this problem as well but it fixed itself when I clicked on edit attributes and typed "bcf" in the Annotation / Notes section. Hope this helps someone. ...
written 2.0 years ago by rquigl0110
0
votes
1
answer
1.1k
views
1
answers
Comment: C: mpileup calling every ALT <X>
... on bcftools view, there is an option to skip sites where the REF field is not A/C/G/T, but my problem is in the ALT column. What option on bcftools are you referring to? ...
written 2.0 years ago by rquigl0110
0
votes
1
answer
989
views
1
answers
Comment: C: Joining multiple fastq files that are spread across two lanes
... Thank you for your help! ...
written 2.0 years ago by rquigl0110
1
vote
1
answer
1.1k
views
1
answer
mpileup calling every ALT <X>
... Im using the mpileup application on galaxy and every base is being called with the ALT . It has 110,000,000 lines as well which seems to be too much. I'm just trying to call SNPs and INDELS. Here is a screenshot. https://gyazo.com/f70ca31ebd7d47421b4e702ae3cb91f3 Does anybody know what I am doing ...
mpileup galaxy written 2.0 years ago by rquigl0110 • updated 2.0 years ago by Jennifer Hillman Jackson25k
0
votes
1
answer
989
views
1
answer
Joining multiple fastq files that are spread across two lanes
... Here is a screenshot of my data https://gyazo.com/90183f5cc58ef9aed362658e24ebf9c1 I know how to concatenate files. I'm just not sure which files I should link together. As you can see from the screenshot, there are 5 R1's from lane one and 5 R1's from lane two. Same scenario for all of the R2's. D ...
galaxy concatenate fastq two lanes written 2.0 years ago by rquigl0110 • updated 2.0 years ago by Jennifer Hillman Jackson25k
0
votes
0
answers
837
views
0
answers
IGV read color question
... What do the colors correspond to on IGV? Most of my reads are red with very few gray and blue colors. What do these colors mean and are they used when variant calling with mpileup? ...
mpileup igv color written 2.0 years ago by rquigl0110

Latest awards to rquigl01

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 16.09
Traffic: 85 users visited in the last hour