User: BioinformaticsLad

Reputation:
150
Status:
Trusted
Location:
Last seen:
4 days, 15 hours ago
Joined:
1 year, 2 months ago
Email:
n****************@gmail.com

Posts by BioinformaticsLad

<prev • 66 results • page 1 of 7 • next >
0
votes
1
answer
149
views
1
answers
Comment: C: Normalizing genes between arrays with Limma
... Thanks Gordon! It does appear that it's an uncommon procedure. I couldn't find direct references to normalizing to genes anywhere. The authors wanted to compare the differential expression of a drug-treated cells vs. untreated control cells. Besides that sentence pasted above, they don't really go ...
written 5 weeks ago by BioinformaticsLad150
3
votes
1
answer
149
views
1
answer
Normalizing genes between arrays with Limma
... I'm working through a paper and it mentions: "[After RMA normalization] ...each gene on the treatment sample arrays were normalised to the median signal intensity of the of the respective gene on the control array." I'm thinking of using `normalizeBetweenArrays` (if that's even the correct function ...
microarray limma written 6 weeks ago by BioinformaticsLad150 • updated 6 weeks ago by Gordon Smyth1.5k
0
votes
1
answer
638
views
1
answers
Comment: C: How does Kraken2 Work?
... Asaf, to your third point, what other methods for contigs would you recommend? I use direct mapping of contigs as an alternative, but that doesn't give me LCA classifications when there's no species hit, which is what I like about Kraken. ...
written 12 weeks ago by BioinformaticsLad150
0
votes
0
answers
111
views
0
answers
Nanopore structural variant calling - more than 2 alleles on IGV track?
... I performed nanopore sequencing on human DNA and ran the Nanopore structural variant calling pipeline (miminmap2 + sniffles) against hg38. I loaded the VCF file into IGV and was surprised to see more than two alleles for most of my chromosomes (especially in the centeromeric regions). What does it m ...
vcf nanopore structural variant igv written 3 months ago by BioinformaticsLad150
0
votes
2
answers
4.6k
views
2
answers
Comment: C: What is the difference between GRCh37 and hs37? And hg19?
... I was under the impression there were slight differences. If it's just a different naming convention, are GRCh38 and hg38 interchangeable? ...
written 4 months ago by BioinformaticsLad150
0
votes
1
answer
221
views
1
answers
Comment: C: Tool to calculate insertion, deletion, mismatch rate in alignments?
... [Alfred][1] turned out to be exactly what I was looking for. [1]: https://github.com/tobiasrausch/alfred ...
written 4 months ago by BioinformaticsLad150
0
votes
1
answer
251
views
1
answers
Comment: C: Detection of antibiotic resistance genes in shotgun metagenomic samples
... I looked in Ariba more and the authors say it's not suitable for metagenomic samples ...
written 5 months ago by BioinformaticsLad150
0
votes
0
answers
140
views
0
answers
BBMap reformat.sh qahist statistics interpretation?
... I ran reformat.sh on a SAM file and the log seemed fine: Input is being processed as unpaired Input: 35583 reads 52857642 bases Output: 35583 reads (100.00%) 52857642 bases (100.00%) But then in the results, the sum of the all matched bases ...
bbmap written 5 months ago by BioinformaticsLad150
2
votes
1
answer
221
views
1
answer
Tool to calculate insertion, deletion, mismatch rate in alignments?
... I know samtools stats can quantify the mismatch rate in SAM files. But are there any tools that can also calculate insertions and deletions? ...
alignment written 5 months ago by BioinformaticsLad150 • updated 5 months ago by h.mon29k
0
votes
2
answers
347
views
2
answers
Comment: C: Filter human parasites from taxonomic profiling with Kraken
... Could you explain why? Do parasites tend to have higher mutation rates? ...
written 6 months ago by BioinformaticsLad150

Latest awards to BioinformaticsLad

Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Guppy basecaller ONT
Supporter 12 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1159 users visited in the last hour