User: Ati

gravatar for Ati
Ati30
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30
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2 days, 11 hours ago
Joined:
3 years, 10 months ago
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Posts by Ati

<prev • 35 results • page 1 of 4 • next >
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UMI on the fastq header
... I have a paired-end bulk RNAseq data. An example of a read header in my data is: ``` @A00379:151:HW2HVDSXX:4:1101:21748:1078_CGCTA 3:N:0:CAGTTCTG+TGACTGAC ``` Based on `@Instrument:RunID:FlowCellID:Lane:Tile:X:Y:UMI ReadNum:FilterFlag:0:IndexSequence or SampleNumber`, **CGCTA** is the UMI. But what ...
illumina umi fastq umi-tools rna-seq written 9 days ago by Ati30
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Comment: C: How to calculate the shortest path between each pairs of genes in WGCNA
... Thanks for the reply. Then which output should be used (Adjacency, TOM or dissTOM)? ...
written 10 months ago by Ati30
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How to calculate the shortest path between each pairs of genes in WGCNA
... I would like to have the shortest path or distance between different pairs of genes in a network constructed by WGCNA R package. ...
wgcna gene co-expression analysis R written 10 months ago by Ati30 • updated 10 months ago by Benn7.9k
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Answer: A: How should I define contrast with more than 2 levels in DESeq2 ?
... You have to use "name" argument in "result" function which is the name of the individual effect (coefficient) for building a results table. Use this argument rather than contrast for continuous variables, individual effects or for individual interaction terms. ...
written 3.1 years ago by Ati30
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Comment: C: Why DESeq2 filter and remove genes with high count?
... If removed genes have high counts in all samples what is your explanation? @WouterDeCoster ...
written 3.2 years ago by Ati30
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Comment: C: Best Way To Quantify Influence Of Different Covariates On Gene Expression?
... Would you please explain more about how to prepare data? ...
written 3.3 years ago by Ati30
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Comment: C: Motifs data base
... Thanks a lot for your information ...
written 3.6 years ago by Ati30
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Comment: C: Motifs data base
... Thanks a lot for your information ...
written 3.6 years ago by Ati30
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Motifs data base
... I have found some motifs using DREME. Is there any database to check whether these motifs report before in specific sequence or region? Thanks ...
dreme motifs rna-seq dna written 3.6 years ago by Ati30 • updated 3.6 years ago by Girolamo140
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Comment: C: Co-variants in differential expression analysis
... Thanks in advance for the nice point ...
written 3.6 years ago by Ati30

Latest awards to Ati

Great Question 10 months ago, created a question with more than 5,000 views. For how to download gene annotation bed file from ensembl?
Great Question 3.1 years ago, created a question with more than 5,000 views. For Bed to BedGraph
Popular Question 3.1 years ago, created a question with more than 1,000 views. For bigwig file in UCSC custom track
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to get sequence using masked repeats?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Pathway analysis using R
Popular Question 3.1 years ago, created a question with more than 1,000 views. For how to download gene annotation bed file from ensembl?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to download intronic positions from Ensembl
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to annotate positions using biomaRt R package?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Convert ensembl gene ID
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Bed to BedGraph

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