User: cxr5298

gravatar for cxr5298
cxr529820
Reputation:
20
Status:
New User
Location:
Last seen:
10 months ago
Joined:
1 year, 11 months ago
Email:
c******@g.rit.edu

Posts by cxr5298

<prev • 6 results • page 1 of 1 • next >
3
votes
2
answers
251
views
2
answers
Automating the creation of IGV style histogram coverage maps
... Hello, I'm working on a pipeline using Bash, Python, and R to process metagenomic datasets. One of the features I want to incorporate is producing coverage maps for some hits depending on the read counts associated with them. I know how to do this using IGV or UCSC genome browser and the necessary ...
genome R alignment python bash written 11 months ago by cxr529820 • updated 11 months ago by dariober11k
0
votes
1
answer
279
views
1
answers
Comment: C: One read and One alignment
... In the case where the read aligns twice to the same species I'd consider it a single 'hit' for the species in question. In the case where a read aligns to multiple species it would be something I'd need to investigate further to determine it's origin. I'm more preoccupied with identifying origin of ...
written 13 months ago by cxr529820
0
votes
1
answer
279
views
1
answers
Comment: C: One read and One alignment
... As far as I can tell the alignments appear valid just that there's more than there should be. This phenomenon is across the board whether I'm using `minmap2`, `bowtie2`, `snap`, or `BWA`. I'm not too familiar with CIGAR strings but from what I can tell the alignments all appear to be good. If I want ...
written 13 months ago by cxr529820
2
votes
1
answer
279
views
1
answer
One read and One alignment
... I am working with a data set of ONT MinION metagenome data aligning it against a fasta file where each entry is a different species using a series of aligners (BWA, Bowtie2, SNAP, and Minimap2) to see which aligner yields the best results. However for each alinger I am getting more alignments to the ...
genome next-gen metagenome rna-seq sequencing written 13 months ago by cxr529820 • updated 13 months ago by swbarnes27.8k
0
votes
0
answers
685
views
0
answers
Comment: C: DESeq2 Long Read RNA, normalization, and interpreting expression data
... I'm working with two replicates of an uninfected control, and 8h, 24h, 48h infected samples. Already this is disqualifying in terms of experimental design but due to unfortunate circumstance this is all the data I have to work with for the time being. ...
written 23 months ago by cxr529820
0
votes
0
answers
685
views
0
answers
DESeq2 Long Read RNA, normalization, and interpreting expression data
... Hello, I am working on getting differential gene expression between an infected and uninfected population using direct RNA-seq from a MinION. When loading my values into DESeq and creating a heatmap and MAplot things look strange and I'm not entirely clear on how to interpret it. My MAplot: [Graph ...
R rna-seq sequencing written 23 months ago by cxr529820

Latest awards to cxr5298

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: 1347 users visited in the last hour