Moderator: Goutham Atla

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Goutham Atla7.2k
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geek_y
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Computational Biology. Marie-Curie ESR. Regulatory genomics. Beta-cell biology. 

Posts by Goutham Atla

<prev • 1,171 results • page 1 of 118 • next >
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Comment: C: A error occurred in the ngsplot analysis.
... you can post the reason. might be helpful for others. ...
written 18 days ago by Goutham Atla7.2k
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Comment: C: How to calculate the different expression gene used PacBio full-length cDNA seq
... As far as I know, if you have the PacBio full-length cDNA , you already have the transcripts. Most of the PacBio analysis tools generates a GTF file at the end. I would generate the gene models from the transcript models and quantify the genes using illumina reads to get the expression levels of gen ...
written 18 days ago by Goutham Atla7.2k
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Comment: C: A error occurred in the ngsplot analysis.
... Workaround: Index the bam file using samtools, and make sure both bam and index are in same folder. Most of the tools tries to index bam only if there is no index available. Regarding the error, give more details about the error. There could be several reasons why a bam file can not be indexed. ...
written 18 days ago by Goutham Atla7.2k
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Comment: C: What are the best tools for differential detection between ATAC-seq samples?
... Did you do PCA analysis on your replicate samples ? ...
written 4 weeks ago by Goutham Atla7.2k
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Comment: C: Single-end control & Paired-end sample in Chip-seq
... As Devon suggested, I always consider R1 and ignore R2 if a sample is paired-end and rest of the samples are single-ended. This should not be a major problem in calling peaks or quantifying the peaks as far as I know. ...
written 6 weeks ago by Goutham Atla7.2k
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Comment: C: using DREME and .broadpeak file
... What kind of Chip-Seq data it is ? ...
written 8 weeks ago by Goutham Atla7.2k
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Comment: C: What are the best tools for differential detection between ATAC-seq samples?
... feautureCounts should do the trick. It has an R interface or command line version. You need to convert your peak coordinates to SAF format as given on their website. ...
written 9 weeks ago by Goutham Atla7.2k
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Comment: C: Picard vs samtools rmdup
... post exact commands and `samtools flagstat` output before and after removing duplicates ...
written 12 weeks ago by Goutham Atla7.2k
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Comment: C: Calling peaks with macs2 if not all replicates have a corresponding input-file
... Its need not be scaling treatment to control always. It scales the sample with large number of reads to sample with smaller number of reads. ...
written 12 weeks ago by Goutham Atla7.2k
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Comment: C: Calling peaks with macs2 if not all replicates have a corresponding input-file
... I would pool all control samples and call peaks on each treatment sample independently. macs2 callpeak -t tfile1.bam -c ctrl_pooled.bam ...
written 12 weeks ago by Goutham Atla7.2k

Latest awards to Goutham Atla

Epic Question 16 days ago, created a question with more than 10,000 views. For Understanding Samtools Flagstat Output
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Google genomics cloud platform ?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Great Question 9 weeks ago, created a question with more than 5,000 views. For Understanding Samtools Flagstat Output
Scholar 9 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: htseq-count for RNA Seq
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Popular Question 4 months ago, created a question with more than 1,000 views. For Annotation Bed File For Phaseolus Vulgaris
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 4 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
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Popular Question 4 months ago, created a question with more than 1,000 views. For Confusion In Pdb File Format
Scholar 5 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Popular Question 5 months ago, created a question with more than 1,000 views. For Confusion In Pdb File Format
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 6 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Popular Question 6 months ago, created a question with more than 1,000 views. For Confusion In Pdb File Format
Scholar 6 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Scholar 7 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise

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