User: Ulduz

gravatar for Ulduz
Ulduz20
Reputation:
20
Status:
New User
Location:
Istanbul
Scholar ID:
Google Scholar Page
Last seen:
1 week ago
Joined:
5 years, 6 months ago
Email:
u***********@gmail.com

Graduate Student of Molecular Biology and Genetics, Bogazici University Laboratory of Genome Regulation

Posts by Ulduz

<prev • 7 results • page 1 of 1 • next >
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Comment: C: DESeq2 Error: Error: $ operator is invalid for atomic vectors
... For this one I used tx2gene with tximport data. Which has the transcript version... (the YY part) ...
written 11 days ago by Ulduz20
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DESeq2 Error: Error: $ operator is invalid for atomic vectors
... Hi, I am using Salmon+DEseq2 for differential expression analysis. No matter wha I change, I always get the same error running the following DEseq command: > dds <- DESeq(ddsTxi, parallel = TRUE, BPPARAM = 7) estimating size factors using 'avgTxLength' from assays(dds), correc ...
tximport deseq2 rna-seq written 12 days ago by Ulduz20
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Answer: A: macs2 output-narrowpeak file understanding?
... The 5th column is for UCSC browser display only. So in UCSC, you will see the stronger peaks darker and weaker peaks lighter. ...
written 3.6 years ago by Ulduz20
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Remove Blacklist regions from ChIP-seq Data
... Hi, In order to get rid of false positive peaks, I want to filter out blacklist region after alignment with Bowtie... I've search and there are three different bed files for Blacklist regions. So which of them is the best choice for TF ChIP-seq data? http://www.broadinstitute.org/~anshul/projects/ ...
chip-seq written 4.9 years ago by Ulduz20 • updated 4.9 years ago by Alex Reynolds29k
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Comment: C: Large Number Of Macs Negative Peaks
... I am having similar problem with my some of my samples (more negative peaks than positive peaks), I am curious to know how did you proceed? ...
written 4.9 years ago by Ulduz20
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Comment: C: Too many suppressed reads
... In different tutorials I have seen they are using n mode for aligning? why are you preferring v mode? ...
written 4.9 years ago by Ulduz20
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Too many suppressed reads
... Hi, I am new to the field. So during analyzing my ChIP-seq results I realized in some of my samples only 50% of my reads are uniquely aligned and around 30-40% of my reads are suppressed reads! Suppressed reads contain reads which are aligned to more than one region on genome.  For aligning I am usi ...
chip-seq written 4.9 years ago by Ulduz20 • updated 4.9 years ago by Manvendra Singh2.1k

Latest awards to Ulduz

Popular Question 4.8 years ago, created a question with more than 1,000 views. For Remove Blacklist regions from ChIP-seq Data
Autobiographer 5.5 years ago, has more than 80 characters in the information field of the user's profile.

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