User: salamandra
salamandra • 230
- Reputation:
- 230
- Status:
- Trusted
- Location:
- Last seen:
- 5 months, 1 week ago
- Joined:
- 4 years ago
- Email:
- t*************@gmail.com
Posts by salamandra
<prev
• 203 results •
page 1 of 21 •
next >
0
votes
2
answers
614
views
2
answers
... thank you very much! ...
written 6 months ago by
salamandra • 230
6
votes
2
answers
614
views
2
answers
... Hi,
I want to access an archived version of biomart and select the human dataset.
mart=useMart("ensembl_mart_92",host="http://apr2018.archive.ensembl.org")
works but if I do:
mart=useMart("ensembl_mart_92",host="http://apr2018.archive.ensembl.org", dataset = "hsapiens_gene_ensembl")
it gi ...
written 6 months ago by
salamandra • 230
• updated
6 months ago by
Mike Smith • 1.2k
0
votes
1
answer
1.7k
views
1
answers
... thanks
So, should I remove duplicate reads in case of chip-seq or is it like as rna-seq that is still on discussion? ...
written 6 months ago by
salamandra • 230
0
votes
1
answer
1.7k
views
1
answers
... Removing duplicate reads does not prevent duplicate alignements? ...
written 6 months ago by
salamandra • 230
0
votes
1
answer
1.7k
views
1
answers
... So, I removed duplicates prior to macs2 ( with bbmap clumpify.sh option 'dedupe') cause I was curious of how many reads were left after removing duplicates in fastq files and by mistake I runned macs2 on both the files without duplicates and files with duplicates.
It gave different number of peaks!
...
written 6 months ago by
salamandra • 230
0
votes
1
answer
645
views
1
answers
... sorry, i'm not understanding
we have a table like this:
Table
sampleName fileName genotype condition group
1 AI_s1 A1_ATCACG_counts I A AI
2 AI_s2 A2_TGACCA_counts I A AI
3 AII_s1 A3_CAGATC_counts II A ...
written 6 months ago by
salamandra • 230
0
votes
1
answer
997
views
1
answers
... Thank you for the answer and the video on DESeq2 normalization
...
written 6 months ago by
salamandra • 230
3
votes
1
answer
997
views
1
answer
... Hi,
1- In the table ´Normalization method' [here][1] says that CPM (counts per million) can be used for gene count comparisons between replicates of the same sample group.
1.1 Does it mean that for eg. we can compare one gene from a sample of group 'control' with same gene of another 'control' sam ...
written 6 months ago by
salamandra • 230
• updated
6 months ago by
ATpoint ♦ 19k
0
votes
1
answer
645
views
1
answers
... Thank you for your time.
From what you pointed to in theDESeq2 vignette I intrepert as `time_t1_vs_t0` is time t1 vs t0 for the refference level (`Untreat`)
Looking at the example in the vignette (easier to understand).
To test if the condition effect (A vs B) varies with genotype (genotype II vs ...
written 6 months ago by
salamandra • 230
0
votes
0
answers
492
views
0
answers
... I have chip-seq peaks and want to find genes to wich they annotate using homer annotatepeaks.pl.
Homer only has pre-built UCSC versions of genome and anotation (not ensembl).
As I'm working with ensembl files, I had to first load ensembl genome and annotation into homer:
loadGenome.pl -name ...
written 7 months ago by
salamandra • 230
Latest awards to salamandra
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Replace discontinued genes by the new ones programaticaly
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Great Question
8 months ago,
created a question with more than 5,000 views.
For Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question
10 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question
10 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Voter
11 months ago,
voted more than 100 times.
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Scholar
11 months ago,
created an answer that has been accepted.
For A: How to select a gene annotation file in ensembl that contain un-localized scaffo
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Centurion
12 months ago,
created 100 posts.
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
Supporter
20 months ago,
voted at least 25 times.
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
Student
2.1 years ago,
asked a question with at least 3 up-votes.
For Install DESeq2 and edgeR with Anaconda
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1580 users visited in the last hour