User: slapiiv

gravatar for slapiiv
slapiiv40
Reputation:
40
Status:
New User
Location:
Last seen:
3 weeks, 6 days ago
Joined:
2 years, 3 months ago
Email:
s******@hotmail.com

Posts by slapiiv

<prev • 12 results • page 1 of 2 • next >
2
votes
3
answers
190
views
3
answers
Answer: A: know the grep command for fastq file
... grep 'HISEQ:151:HHKH7BCXX:2:1203:18952:80029' your_fastq_file.fastq ...
written 5 weeks ago by slapiiv40
0
votes
1
answer
145
views
1
answers
Comment: C: How to proceed after removing batch effect with limma?
... Thanks Pietro, I have found the answer: dds <- DESeq(dds, test="LRT", reduced=~batch) ...
written 6 weeks ago by slapiiv40
0
votes
1
answer
145
views
1
answers
Comment: C: How to proceed after removing batch effect with limma?
... Thanks h.mon, so, basically I just can remove it for visualization but not for the calculation of DE? ...
written 6 weeks ago by slapiiv40
2
votes
1
answer
145
views
1
answer
How to proceed after removing batch effect with limma?
... Hi everyone, I have visualized some batch effects in my sequencing replicates and I have removed with the limma package as follows. mat <- limma::removeBatchEffect(mat, vsd$batch) After that, batch effect has been at least minimized and the PCA looks very good as I expected, however, at thi ...
batch-effect deseq2 limma rna-seq written 6 weeks ago by slapiiv40 • updated 6 weeks ago by Pietro90
0
votes
1
answer
207
views
1
answers
Comment: C: bowtie --best, what exactly does it mean?
... Oh I see, bowtie is a bite confusing anyways, but I have undesrstand my specific doubt. Thanks. ...
written 4 months ago by slapiiv40
1
vote
1
answer
207
views
1
answers
Comment: C: bowtie --best, what exactly does it mean?
... Thanks, the answer that I was looking for is: a strata is a set of alignments where mismatches occur at identical positions. For example, suppose there are two 1-mismatch hits. One with the mismatch at 7th position and the other at the 9th position. The two hits are in two different strata. ...
written 4 months ago by slapiiv40
0
votes
1
answer
183
views
1
answers
Comment: C: Dual rnaseq normalization
... Nice, I will take a look but it seems very useful, thanks. ...
written 4 months ago by slapiiv40
5
votes
1
answer
207
views
1
answer
bowtie --best, what exactly does it mean?
... Hi, everybody: I am using bowtie for aligning smallRNAseq reads against a genome reference, I am using *--best* because it is recommended for miRNAs, but as you may know the bowtie`s manual is not clear enough as we the beginners need. Does somebody know what does it exactly means? --best ...
bowtie rna-seq mapping written 4 months ago by slapiiv40 • updated 4 months ago by Charles Warden7.2k
1
vote
1
answer
183
views
1
answer
Dual rnaseq normalization
... Hi everybody, I have performed a dual rnaseq (infected cells by a pathogen) at different points, at the beginning host-corresponding reads are more than 90% of the total, however, at a later point, I have almost 50% or reads corresponding to the host and 50% corresponding to the protozoo (total rea ...
normalization rna-seq written 4 months ago by slapiiv40 • updated 4 months ago by grant.hovhannisyan1.7k
0
votes
0
answers
7.7k
views
0
answers
Comment: C: Find number of rows contain zero raw count across all sample (column) using R
... If my answer was helpful you should upvote it, ...
written 2.2 years ago by slapiiv40

Latest awards to slapiiv

Supporter 15 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: 814 users visited in the last hour