User: Aurelie MLB

gravatar for Aurelie MLB
Aurelie MLB290
Reputation:
290
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Location:
United Kingdom
Last seen:
5 months ago
Joined:
3 years, 11 months ago
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Posts by Aurelie MLB

<prev • 67 results • page 1 of 7 • next >
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Best current ways to find TSS please (even cell dependent ones)?
... Hello, I am trying to map the TSS of genes in the whole genome. I did look for what people were proposing already but the last posts on this subject are quite old. I was wondering if the current view would be different. Examples of what I have seen so far are: - mapping to GencodeV19/Ensembl relea ...
genome written 5 months ago by Aurelie MLB290
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Comment: C: Quick question: samtool idxstats and multiple mapping
... Thank you so much to both!! Really helpful!! ...
written 6 months ago by Aurelie MLB290
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Quick question: samtool idxstats and multiple mapping
... Hello, A quick naive question please: Samtools idxstats outputs the number of reads mapped to a given reference sequence. Right? What does it do in case of multiple mapping please? Does it count the best alignment for a read or does it adds 1 to all reference sequences where it mapped? I could not ...
alignment sequencing written 6 months ago by Aurelie MLB290 • updated 6 months ago by Devon Ryan79k
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Comment: C: [Should I used CAGE?]: gene set enrichment analysis on image analysis experiment
... Thanks a lot! This is helpful. ...
written 11 months ago by Aurelie MLB290
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[Should I used CAGE?]: gene set enrichment analysis on image analysis experimental values
... Hello, I have experimental values for a large set of genes that are NOT coming from sequencing. They are image analysis derived GFP intensities. From these values, some of those genes are interesting and some are not so I could if needed define a set of "interesting" genes. But I would prefer to ta ...
gene pathway bioprocess written 11 months ago by Aurelie MLB290 • updated 11 months ago by Jean-Karim Heriche15k
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Comment: C: RNA-seq: how big should be the library?
... Hello, May I ask a stupid question please? I would like to double check. When someone talk about the "size of the library", does he means the number of forward reads PLUS the number of reverse reads? Or does he mean the number of templates (i.e. == Number of forward reads) please? ...
written 2.1 years ago by Aurelie MLB290
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Comment: C: Ideal size of a library for miRNA ?
... Thank you ! ...
written 2.3 years ago by Aurelie MLB290
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Ideal size of a library for miRNA ?
... Hello, I was wondering what is your experience about miRNA sequencing please? What would be the ideal size for a library? I found this documentation from Exiqon (http://www.exiqon.com/ls/Documents/Scientific/Service-Customer-Information-NGS.pdf) basically saying that 5 M reads should be sufficient ...
rna-seq written 2.3 years ago by Aurelie MLB290 • updated 2.3 years ago by Chris Fields1.9k
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Answer: A: DESeq2: why the independent filtering threshold would come back as NULL please?
... Hello, I have found the answer to my question. In the updated vignette, it is explained that the filtering threshold can be obtained by: metadata(RES)$filterThreshold. RES being what is returned by the "results" function. So I guess my code was out of date. Thanks ...
written 2.3 years ago by Aurelie MLB290
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Comment: C: Sailfish TPM normalization: does it take into account the size the library?
... Thank you very much! ...
written 2.3 years ago by Aurelie MLB290

Latest awards to Aurelie MLB

Popular Question 6 months ago, created a question with more than 1,000 views. For GRCh38 Annotation for non coding RNA (e.g. miRNA)
Popular Question 11 months ago, created a question with more than 1,000 views. For In R bioconductor, how to combine DNAString views please ?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For In R bioconductor, how to combine DNAString views please ?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to link UCSC transcripts ids to protein ids using bioconductor ?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For DESeq2 normalisation: is the size of the gene taken into account?
Good Question 2.6 years ago, asked a question that was upvoted at least 5 times. For RNA-seq: how big should be the library?
Supporter 2.9 years ago, voted at least 25 times.
Appreciated 3.0 years ago, created a post with more than 5 votes. For RNA-seq: how big should be the library?
Student 3.1 years ago, asked a question with at least 3 up-votes. For RNA-seq: how big should be the library?

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