User: salamandra
salamandra • 180
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Posts by salamandra
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... thank you very much! ...
written 10 weeks ago by
salamandra • 180
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... 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I want to access an archived version of biomart and select the human dataset.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 10 weeks ago by
salamandra • 180
• updated
10 weeks ago by
Mike Smith • 1.1k
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... 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 10 weeks ago by
salamandra • 180
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... Removing duplicate reads does not prevent duplicate alignements? ...
written 10 weeks ago by
salamandra • 180
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... 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 11 weeks ago by
salamandra • 180
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... 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 11 weeks ago by
salamandra • 180
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... Thank you for the answer and the video on DESeq2 normalization
...
written 11 weeks ago by
salamandra • 180
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... 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 11 weeks ago by
salamandra • 180
• updated
11 weeks ago by
ATpoint ♦ 14k
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... 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 11 weeks ago by
salamandra • 180
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... 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 3 months ago by
salamandra • 180
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