User: codezy

gravatar for codezy
codezy10
Reputation:
10
Status:
New User
Location:
germany
Last seen:
2 days, 8 hours ago
Joined:
3 months, 2 weeks ago
Email:
y**************@gmail.com

Posts by codezy

<prev • 6 results • page 1 of 1 • next >
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How to get a annotation from ucsc table browser which include intron, exon and 5'/3' UTR ?
... Dear all, I would like to get an annotation file (which is in gtf or bed format) for a list of genes. And this annotation should include the information of intron, exon, 3' UTR and 5' UTR. Could anyone give me some tips on how can I do that? Thank you ...
genome written 17 days ago by codezy10 • updated 17 days ago by genomax65k
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Comment: C: Will the --outfiltermismatchNmax in the STAR works for the single end reads?
... @ATpoint Thank you for your answer. I have also read this int, but in page 9 of STAR manual they said "--outFilterMismatchNmax 999 maximum number of mismatches per pair, large number switches off this lter" So I confused about that. ...
written 3 months ago by codezy10
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Will the --outfiltermismatchNmax in the STAR works for the single end reads?
... Dear all, I have some single end reads and I would like to do the mapping step with STAR. But depends on the manual of STAR the -- outFilterMismatchNmax is for setting the maximum number of mismatches per pair. So I was wondering if this --outFilterMismatchNmax will also work for the single end rea ...
alignment rna-seq written 3 months ago by codezy10 • updated 3 months ago by ATpoint15k
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Answer: A: I meet some problem for using Deseq2.
... Thank you for all your answer. I have solved the problem by these codes: sampleFiles <- grep("count",list.files("F:/"),value=TRUE) sampleCondition <- sub("(.*count).*","\\1",sampleFiles) sampleTable <- data.frame(sampleName = sampleFiles, fileName = sampleFiles, condition = s ...
written 3 months ago by codezy10
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Comment: C: I meet some problem for using Deseq2.
... I have solved the problem with these codes`sampleFiles <- grep("count",list.files("F:/"),value=TRUE) sampleCondition <- sub("(.*count).*","\\1",sampleFiles) sampleTable <- data.frame(sampleName = sampleFiles, fileName = sampleFiles, condit ...
written 3 months ago by codezy10
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I meet some problem for using Deseq2.
... Dear all, I am new in this area and trying to learn how to do the differential analysis now. I have got some bam file from the mapping tool STAR. Now I want to use the DESeq2 to continue the analysis, but DESeq2 ask a matrix as input. Therefore, I use htseq-count to convert the reads bam file into ...
rna-seq written 3 months ago by codezy10

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