Moderator: geek_y

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I work with range of genomic data like transcriptome (RNA-Seq, CAGE-Seq), open chromatin/histone modifications/TF profiles, chromosome contact maps etc to understand tissue specific transcriptional regulation in human genome.

 

Posts by geek_y

<prev • 1,302 results • page 1 of 131 • next >
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Comment: C: Should I quit PhD program?
... Basically, OP is not sure about quitting, so he came here and seeking suggestions. We could be positive and provide realistic solutions. ...
written 6 days ago by geek_y8.5k
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Answer: C: Should I quit PhD program?
... Is there a possibility that you could use bioinformatics skills in your project and make it multidisciplinary ? Or you could also discuss with your PI and ask if he could involve you in other collaborative projects that are more focused on bioinformatics ? There is a lot of data out there and you ...
written 6 days ago by geek_y8.5k
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Answer: A: how can I compare two samples of RNA-seq Generally
... Quantify the gene/transcripts --> normalize (TPM/TMM/FPKM/RPKM) and do a Spearman's correlation. If you dont have annotations, use stringtie to assemble transcript structures. ...
written 18 days ago by geek_y8.5k
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Comment: C: Java TreeView like tools
... Honestly, I liked the previous version. It looks very complicated now. ...
written 19 days ago by geek_y8.5k
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Comment: C: Phased Genome, Want reads From Both Alleles
... Point 4 is quite demanding. People help whichever way they can. ...
written 20 days ago by geek_y8.5k
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Answer: A: Phased Genome, Want reads From Both Alleles
... Use [ASEReadCounter][1] from GATK. [1]: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_rnaseq_ASEReadCounter.php ...
written 20 days ago by geek_y8.5k
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Comment: C: List of TSS from GTF file
... Are you just pulling the start position of each entry (each line) in GTF ? ...
written 21 days ago by geek_y8.5k
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Comment: C: Do I have to mark duplicates before mapping the reads
... MarkDuplicates is done after alignment ...
written 22 days ago by geek_y8.5k
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Answer: A: Do I have to mark duplicates before mapping the reads
... I guess when you say "duplicates before mapping", you mean reads with identical sequences. You don't need to. And in RNA-Seq, its not usual to remove duplicate reads. ...
written 23 days ago by geek_y8.5k
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Comment: C: split vcf, choice
... If that particular sample doesn't contain a variant i.e either not called or "reference homozygous", it will not be printed, which makes sense. ...
written 23 days ago by geek_y8.5k

Latest awards to geek_y

Popular Question 5 days ago, created a question with more than 1,000 views. For RUVSeq normalisation: Pairing information as a factor
Scholar 5 days ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Student 5 days ago, asked a question with at least 3 up-votes. For What is the best way to handle unmapped reads from RNA-Seq data
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Commentator 6 days ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Popular Question 10 days ago, created a question with more than 1,000 views. For RUVSeq normalisation: Pairing information as a factor
Scholar 20 days ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Good Answer 26 days ago, created an answer that was upvoted at least 5 times. For A: htseq-count for RNA Seq
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: htseq-count for RNA Seq
Appreciated 3 months ago, created a post with more than 5 votes. For Informatics of RNA-Seq.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Great Question 5 months ago, created a question with more than 5,000 views. For Where can I download the blast version that includes formatdb ?
Popular Question 6 months ago, created a question with more than 1,000 views. For Google genomics cloud platform ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Is this RNA-seq data reliable?
Popular Question 6 months ago, created a question with more than 1,000 views. For Google genomics cloud platform ?
Popular Question 6 months ago, created a question with more than 1,000 views. For Google genomics cloud platform ?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Scholar 8 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Popular Question 8 months ago, created a question with more than 1,000 views. For Google genomics cloud platform ?

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