User: Anna

gravatar for Anna
Anna90
Reputation:
90
Status:
Trusted
Location:
Last seen:
2 months ago
Joined:
9 years, 3 months ago
Email:
a***********@gmail.com

Posts by Anna

<prev • 7 results • page 1 of 1 • next >
0
votes
4
answers
4.1k
views
4
answers
Answer: A: Changing names of Fasta headers
... I worked out another solution using a combination of AWK, SED and Perl. This solution works for single files, where each file has one header and the goal is to replace the header with a modified version of the file name. Assuming all your fasta files in the current directory end in ".fa", run the ...
written 3 months ago by Anna90
5
votes
1
answer
2.3k
views
1
answers
Answer: A: What the heck is going on with this DESeq2 MA Plot?
... I had the same problem, but not necessarily linked to a previous PCA plot. In my case, the `plotMA` function was being called from a different package. Be aware that there are many packages that have a `plotMA` and not all of them take the same class of object. I solved it by using `DESeq2::plotMA ...
written 7 months ago by Anna90
0
votes
1
answer
716
views
1
answers
Answer: A: Truseq Stranded Total RNA and NEBNext Ultra II Directional RNA library prep kit
... Hi, if you encounter batch effects with your samples due to using different library preps, you can have a go at removing unwanted variation using Ruvseq. https://bioconductor.org/packages/release/bioc/html/RUVSeq.html A great lecture on the effect of using Ruvseq: https://vimeo.com/299777276 ...
written 11 months ago by Anna90
1
vote
1
answer
2.0k
views
1
answers
Answer: A: What Mapping Quality Read Should I Use For Down Stream Rna-Seq Analysis
... hi I restrict my mapping quality (-q option in samtools) by 30. and it seems to work OK to me. Your option 4 looks the best from the ones you presented here. You def don't one none-unique reads in rna-seq!! good luck Anna ...
written 8.9 years ago by Anna90
0
votes
6
answers
12k
views
6
answers
Answer: A: Gencode Gtf To Bed12 Or Psl
... hi, I am having the same problem to convert from gff to bed12 - since the latter is a requirement for coverageBed -split. any ideas? or should I write my own thing? thanks! Anna ...
written 8.9 years ago by Anna90
2
votes
1
answer
2.6k
views
1
answers
Answer: A: Refining My Transcriptome Assembly
... hi Craig, there are several ways or reducing redundancy. for example, if you have a draft assembly you can use the reads mapped to individual contigs to reduce the possible reads that velvet/oases uses. You'd be running one velvet-oases for each contig using ONLY the reads mapping to that contig. Th ...
written 9.0 years ago by Anna90
1
vote
1
answer
1.4k
views
1
answers
Answer: A: Are Old 454 Ls Rna-Seq Reads 5'-Biased Or 3'-Biased?
... If you have a protocol of how the sample where generated I can tell you :) ...
written 9.3 years ago by Anna90

Latest awards to Anna

Teacher 7 months ago, created an answer with at least 3 up-votes. For A: What the heck is going on with this DESeq2 MA Plot?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1845 users visited in the last hour