User: siddharth.sethi5

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190
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Medical Research Council, Oxford, United Kingdom
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1 year, 6 months ago
Joined:
5 years, 4 months ago
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s***************@gmail.com

I am a bioinformatician and work on next generation sequencing data. I have experience in analyzing genomic and transcriptomic sequence data

Posts by siddharth.sethi5

<prev • 19 results • page 1 of 2 • next >
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fr-firststrand or not ?
... IGV SNAPSHOT :[2] http://postimg.org/image/4xjcmzorz/ Hello everyone, Quick question, just to confirm, is this fr-firststrand ? Single - end reads , all mapped to the opposite direction of the gene. Thanks [2]: http://postimg.org/image/4xjcmzorz/ ...
strand specific rna-seq single end written 19 months ago by siddharth.sethi5190 • updated 18 months ago by Biostar ♦♦ 20
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Comment: C: Pheatmap Annotation
... Tried with Windows R , it works with windows. There is a bug in Linux version. version = pheatmap_1.0.8 ...
written 21 months ago by siddharth.sethi5190
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Comment: C: Pheatmap Annotation
... Hi , have you tried annotation of the rows. It seems to be not working. Even the column annotation doesnot work if you use the argument "annotation_col" . Using the argument "annotation" defaults to column annotation . So I am not able to get row annotations with "annotation_row" argument. seems li ...
written 21 months ago by siddharth.sethi5190
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Comment: C: How to extract sequences from multz sequence alignment on UCSC genome browser?
... Hi Denise, Can you please tell me how do this using perl API. I am trying to use the code from compara tutorials, but I do not want pairwise alignments , as extracted by this " fetch_by_method_link_type_GenomeDBs(       'LASTZ_NET' )". I want the alignments in multiple species , for example for 17 e ...
written 2.1 years ago by siddharth.sethi5190
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Annotating SNPs for promoter and enhancer regions
... Hi Everyone, I am trying to annotate Snps and identify those snps which fall within promoter and enhancer regions. I am doing this using Mouse ENCODE data and have chromatin data for 23 TISSUES. My question is, In how many tissues a SNP should be found to be annotated as enhancer/promoter to be co ...
enhancer promoter snp written 2.3 years ago by siddharth.sethi5190 • updated 2.2 years ago by Shicheng Guo4.5k
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Comment: C: Different results from Different Cufflinks versions
... Thanks very much guys for the help and suggestions. ...
written 3.3 years ago by siddharth.sethi5190
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Comment: C: Different results from Different Cufflinks versions
... I use DESeq and and EdgeR as well. But I am also interested in the Isoforms and splicing differential expression, thats where I use cufflinks. Do you know about other popular tools for isoform and splicing. I am already using MATS and Bitseq. ...
written 3.3 years ago by siddharth.sethi5190
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Different results from Different Cufflinks versions
... Hi, I have noticed that the newer versions of Cufflinks are giving much more significant differentially expressed genes. I am updating my pipeline, so I am confused whether to use the new version or not. Has anyone validated any results from new version or have any idea about the false positive rat ...
cufflinks rna-seq written 3.3 years ago by siddharth.sethi5190 • updated 3.3 years ago by Charles Warden4.9k
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Comment: C: Snp.Plotter Input Files
... Hi, Can you please tell me how to create a genotype and hapmap file. I just have a ped file which i used for PLINK . ...
written 3.7 years ago by siddharth.sethi5190
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Htseq Count - Gene And Exon Problem
... Hello everyone, I ran HTseq-count to cound reads for each GENE python -m HTSeq.scripts.count -s no input.sam mm9.gtf > output_1 Then I ran it to count reads for each EXON python -m HTSeq.scripts.count -s no -i exon_id input.sam mm9.gtf > output_2 But if I add up the read count for all e ...
gene written 4.5 years ago by siddharth.sethi5190 • updated 3.8 years ago by Biostar ♦♦ 20

Latest awards to siddharth.sethi5

Appreciated 19 months ago, created a post with more than 5 votes. For Rpkm Calculation For Genes
Great Question 20 months ago, created a question with more than 5,000 views. For Should We Remove Duplicated Reads In Rna-Seq ?
Appreciated 21 months ago, created a post with more than 5 votes. For Rpkm Calculation For Genes
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Great Question 3.6 years ago, created a question with more than 5,000 views. For Rpkm Calculation For Genes
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Htseq-Count Not Working With Bam From Tophat
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Should We Remove Duplicated Reads In Rna-Seq ?
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