Moderator: geek_y

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geek_y8.2k
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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

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Comment: C: What are the best tools for differential detection between ATAC-seq samples?
... Its not "noise". ...
written 12 days ago by geek_y8.2k
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Comment: C: What are the best tools for differential detection between ATAC-seq samples?
... Its not because ATAC is more noisy, Its because the open chromatin is not very dynamic unless the cell environment changes drastically. If you compare the ATAC profiles between two different cell types, you will see differential open chromatin regions but may not with in the same cell type exposed t ...
written 13 days ago by geek_y8.2k
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Comment: C: cut mt,x and unknown chromosomes
... Make a bed file with chr coordinates (chromosome length). Intersect VCF with the chr bed file using bedtools. ...
written 5 weeks ago by geek_y8.2k
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Comment: C: perl script to grep a part of header from fasta seq file
... As you are a new user, you should know that first you need to try something yourself, in awk/perl or whatever language, and if you still cant figure out, people help in modifying your script/command. People here doesn't provide ready-made scripts as per your requirements. There are many many posts ...
written 7 weeks ago by geek_y8.2k
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Answer: A: Comparing transcriptomic data of the same species from different developmental s
... There are some softwares designed to handle time series data. Basically you need to do a fuzzy clustering to identify the patterns of gene expression. Few of several are [maSigPro][1], [Mfuzz][2] [1]: https://bioconductor.org/packages/release/bioc/html/maSigPro.html [2]: https://bioconductor.o ...
written 7 weeks ago by geek_y8.2k
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Answer: A: How to choose peak-associated genes for verification of Chip-seq recovered Motif
... If the novel TF is regulating some genes, most probably they would be enriched in a pathway relevant to your study. You need to perform a functional enrichment analysis (GO, pathways, gene sets etc) to identify candidate genes to test for. If the peaks are on the promoters, then its a bit easy as ...
written 7 weeks ago by geek_y8.2k
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Comment: C: Extracting differentially expressed genes in R
... Just a comment, be careful while using filters on logFC vs FC. If you just want to filter on FC, you need to convert that to appropriate log value while filtering. ...
written 7 weeks ago by geek_y8.2k
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Comment: C: Finding difference in read depth between two BAM files
... What data it is ? ChIP ? WGS ? RNA ? ...
written 10 weeks ago by geek_y8.2k
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Comment: C: Tools for finding gene clusters in RNA-seq differential expression data?
... If you have large number of samples ( more than 15 samples per condition ) you can use WGCAN as mentioned by others to find modules of genes. But, if you dont have large samples, I would suggest to use simple clustering methods like hierarchical or k-means clustering. You can use different methods l ...
written 12 weeks ago by geek_y8.2k
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Answer: A: Time series analysis from ChIP-Seq data
... You could use same tools. I saw many papers using DESeq2 or edgeR with any king of counts data generated by high throughput sequencin to identify the differences in two different settings. ...
written 3 months ago by geek_y8.2k

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Good Answer 1 day ago, created an answer that was upvoted at least 5 times. For A: htseq-count for RNA Seq
Appreciated 21 days ago, created a post with more than 5 votes. For Informatics of RNA-Seq.
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Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Is this RNA-seq data reliable?
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Scholar 5 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Popular Question 5 months ago, created a question with more than 1,000 views. For Google genomics cloud platform ?
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Popular Question 5 months ago, created a question with more than 1,000 views. For Google genomics cloud platform ?
Scholar 6 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
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Commentator 6 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
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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
Scholar 6 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
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