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User: Jingyue

gravatar for Jingyue
Jingyue • 30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
2 days, 20 hours ago
Joined:
5 years, 8 months ago
Email:
j***********@uconn.edu

Posts by Jingyue

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Why ranges of narrowPeak file and that of bed file are not identical
... I have been using narrowPeak files for downstream analysis (annotation, motif finding, differential peak calling), should I use the summits.bed or narrowPeak files? I'm asking this because narrowPeak files have many peaks start-end ranges if use --call-summits in MACS2. So I only keep 1 unique peak ...
written 26 days ago by Jingyue • 30
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Comment: C: DESeq2 compare all levels
... Thank you for the help! ...
written 5 weeks ago by Jingyue • 30
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Comment: C: DESeq2 compare all levels
... Hello, Did you solve this? It happens to me as well! Thanks! ...
written 5 weeks ago by Jingyue • 30
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Answer: A: Retrieve genomic physical coordinates of 3'UTR for set of genes
... Download the bed file from the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables). Set the parameters as shown below: - clade: Mammal - genome: Human - assembly: 2009(GRCh37/hg19) - group: Genes and Gene Predictions - track: select the one that fits your experimental pur ...
written 7 weeks ago by Jingyue • 30
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Job: PhD assistantship in animal functional genomics and bioinformatics at Cornell
... Dear Community, We are starting a new lab in College of Agriculture and Life Sciences at Cornell. We will have 2 PhD research assistant positions in animal functional genomics and bioinformatics available at Cornell Animal Science in 2021 Fall (Postdoc positions are also available). Please find our ...
functional genomics next-gen epigenetics job written 3 months ago by Jingyue • 30
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Comment: C: ATAC-seq DE analysis
... Thanks for your answer! I'm wondering do you use DEseq2 or EdgeR for differential analysis on these merged read counts coverage files? I thought they all need sample replicates as input. Thank you! ...
written 11 months ago by Jingyue • 30
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ATAC-seq +4 -5 shift
... Dear all, I saw having the mapped reads have +4 and -5 shift in ATAC-seq is a common practice. Some place says "reads should be shifted + 4 bp and − 5 bp for positive and negative strand respectively, to account for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase and ach ...
atac-seq written 11 months ago by Jingyue • 30 • updated 9 weeks ago by Devon Ryan ♦ 98k
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Comment: C: ATAC-seq 150bp reads
... Hi, ATpoint, Thanks for the insightful answer! I plan to send out my sample for sequencing. Do you think sequencing ATAC library at a short length directly would be better? Like 35bp paired end reads. Or do long reads 150bp and then clip it shorter by some tools? Thank you! ...
written 13 months ago by Jingyue • 30
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Comment: C: Differential Peaks Between Replicates
... Hello, Do you also merge the differential binding regions among these different tools? Thanks! ...
written 17 months ago by Jingyue • 30
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ChIP-seq differential binding analysis tools
... Hello all, Do you recommend to overlap two or more differential peak calling tools to get a more stringent/accurate differential peaks? Thank you! ...
csaw diffbind chip-seq written 17 months ago by Jingyue • 30

Latest awards to Jingyue

Popular Question 10 days ago, created a question with more than 1,000 views. For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question 5 months ago, created a question with more than 1,000 views. For Running Cuffmerge error "duplicate/invalid 'transcript' "
Supporter 19 months ago, voted at least 25 times.
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Running Cuffmerge error "duplicate/invalid 'transcript' "
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