User: salamandra

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salamandra230
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Posts by salamandra

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Comment: C: BiomaRt: archive version of ensembl not working
... thank you very much! ...
written 6 months ago by salamandra230
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BiomaRt: archive version of ensembl not working
... Hi, I want to access an archived version of biomart and select the human dataset.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 ...
R biomart written 6 months ago by salamandra230 • updated 6 months ago by Mike Smith1.2k
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Comment: C: If we use MACS2 do we need to remove duplicate sequences with samtools rmdup ?
... 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 salamandra230
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Comment: C: If we use MACS2 do we need to remove duplicate sequences with samtools rmdup ?
... Removing duplicate reads does not prevent duplicate alignements? ...
written 6 months ago by salamandra230
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Comment: C: If we use MACS2 do we need to remove duplicate sequences with samtools rmdup ?
... 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 salamandra230
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Comment: C: DESeq2 design formula: how to use the opposite interaction term?
... 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 salamandra230
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Comment: C: CPM read count normalization: what does it mean between replicates of same group
... Thank you for the answer and the video on DESeq2 normalization ...
written 6 months ago by salamandra230
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CPM read count normalization: what does it mean between replicates of same group and within same replicate?
... 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 ...
read count normalization rna-seq written 6 months ago by salamandra230 • updated 6 months ago by ATpoint19k
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Comment: C: DESeq2 design formula: how to use the opposite interaction term?
... 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 salamandra230
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Homer: annotate peaks with ensembl annotation (.gtf) file instead of UCSC anotation file?
... 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 ...
homer annotatepeaks.pl written 7 months ago by salamandra230

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