User: Krish Srinivasan

Reputation:
20
Status:
New User
Location:
Canada
Last seen:
3 months ago
Joined:
3 years, 8 months ago
Email:
s******@mcmaster.ca

I am a Master's student with a background in Biology but starting to use more Bioinformatic approaches in my research. 

Posts by Krish Srinivasan

<prev • 22 results • page 1 of 3 • next >
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Comment: C: HT-seq Counts Stranded option
... Hi, please take a look at this for an explanation https://www.preprints.org/manuscript/201903.0124/v1 ...
written 3 months ago by Krish Srinivasan20
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Comment: C: Many DESeq2 P values are 0 thus preventing generation of a rank list for GSEA
... Thanks for the article, I'm sure it will be very helpful! ...
written 2.3 years ago by Krish Srinivasan20
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Many DESeq2 P values are 0 thus preventing generation of a rank list for GSEA
... Hi Everyone, In my DESeq2 reuslts files, the smallest 100 P-values are 0 (as the smallest floating point value in R is 2.225074e-308). I am wondering if there is any way to discern the unrounded values of these P-values as they are needed in order for me to produce a rank list for gene set enrichm ...
gene R rna-seq written 2.3 years ago by Krish Srinivasan20 • updated 2.3 years ago by Martombo2.6k
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Older Microarray probes not matching Ensembl genes
... Hello, I have some old microarray data from a zebrafish experiment done years ago. The probes are Agilent G2519f. When i input a small subset of probes into Biomart on ensembl to get genes, over half of these probes do not seem to be representing a gene. Is there some way to update the probes to t ...
gene genome written 3.2 years ago by Krish Srinivasan20
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Comment: C: Tophat2 Accepted hits Visualization and HT-seq Count not agreeing
... Looking through, I know that Union is the mode I need. However how can I visualize if these reads are are overlapping 2 genes? ...
written 3.3 years ago by Krish Srinivasan20
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Comment: C: Tophat2 Accepted hits Visualization and HT-seq Count not agreeing
... Yeah, I notice that also. But I also see reads aligning to exons, therefore stranded = reverse should be giving some counts correct? Unless all these reads are being labelled as ambiguous due to overlapping another gene on the other strand? ...
written 3.3 years ago by Krish Srinivasan20
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Comment: C: Tophat2 Accepted hits Visualization and HT-seq Count not agreeing
... In tablet, how can I tell which strand a read pair is mapping to? The odd thing is that for other genes on the reverse strand, HT-seq count seems to be counting them. ...
written 3.3 years ago by Krish Srinivasan20
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Comment: C: Tophat2 Accepted hits Visualization and HT-seq Count not agreeing
... I already tried that, but its doesn't make a difference. I think I read somewhere that the --fr firststrand in tophat only edits XS flags? ...
written 3.3 years ago by Krish Srinivasan20
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Comment: C: Tophat2 Accepted hits Visualization and HT-seq Count not agreeing
... I am using the galaxy version of HT-seq Count. Here is the Job Command Line samtools sort -n "/galaxylab/production/new/galaxy/database/files/000/dataset_392.dat" "name_sorted_alignment" && htseq-count --mode=union --stranded=reverse --minaqual=10 --type="exon" --idattr="gene_id" --order=n ...
written 3.3 years ago by Krish Srinivasan20
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Tophat2 Accepted hits Visualization and HT-seq Count not agreeing
... Hi all, I seem to be have problems with Tophat2 or HT-seq counts. I am visualizing the tophat BAM file using Tablet. The trouble is, there seems to be reads aligning to this specific gene (spi-c, zebrafish, reverse strand) however HT-seq counts (using stranded = reverse) is counting 0 reads for th ...
tophat2 ht-seq count rna-seq written 3.3 years ago by Krish Srinivasan20

Latest awards to Krish Srinivasan

Great Question 2.0 years ago, created a question with more than 5,000 views. For Get normalized count Data using DESeq2 in R
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Ht-seq count stranded=Yes question
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Get normalized count Data using DESeq2 in R
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Tophat2 Accepted hits Visualization and HT-seq Count not agreeing
Popular Question 2.0 years ago, created a question with more than 1,000 views. For HT-seq Counts Very High Number of No Feature
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Many DESeq2 P values are 0 thus preventing generation of a rank list for GSEA
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Get normalized count Data using DESeq2 in R
Autobiographer 3.4 years ago, has more than 80 characters in the information field of the user's profile.

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