User: Anil Kesarwani

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80
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United States
Last seen:
2 years, 1 month ago
Joined:
5 years, 2 months ago
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Posts by Anil Kesarwani

<prev • 27 results • page 1 of 3 • next >
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MISO: Extraction of splicing events from user specified gene annotation (gtf or gff)
... Hi, - MISO comes with its own set splicing events, which are used by MISO for event-specific PSI calculation. - For event-centric analysis, does MISO provide any tool for the extraction of splicing events from user specified gene annotation (gtf or gff) and prepare input for MISO. It would be extrem ...
miso rna-seq written 2.3 years ago by Anil Kesarwani80 • updated 11 months ago by deshpandenandan19750
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Comment: C: CLIP-Seq read density
... Thanks for your suggestion. In the RSeqQC, I dont find any option for normalizing the read count for the specific region by gene expression (FPKM already calculated). I have conducted CLIP-Seq and the RNA-Seq (for normalization) for the sample in 3 replicates. Using an approach similar to RSeqQC, I ...
written 3.3 years ago by Anil Kesarwani80
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CLIP-Seq read density
... Dear Bioinfo Geeks, I have obtained CLIP-Seq read coverage, which is mostly sequestered in 3’ UTR with relatively much lesser density in the CDS and 5’ UTR ([Example][1]). This scenario is true for almost all genes I looked. I am struggling to find a way to represent this pattern for all genes in o ...
rna-seq written 3.3 years ago by Anil Kesarwani80 • updated 3.3 years ago by genomax71k
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Normalization of CLIP peak by transcript level
... HI, I am using Piranha for CLIP-Seq data analysis. I was wondering how to normalize peaks by transcript  abundance (calculated as FPKM from RNA-seq). I read in several articles that normalization with transcript level could help remove spurious peaks. I therefore performed RNA-seq as well, together ...
tool rna-seq written 3.6 years ago by Anil Kesarwani80 • updated 3.6 years ago by Istvan Albert ♦♦ 81k
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How to calculate differential usage of splice junction
... Hi, Could some body please guide me about how to calculate differential usage of splice junction between two samples. I have read count information for each junction detected from TopHat2 alignment. The samples are in replicates, so P-value and FDR will be needed to select significant differentiall ...
tool rna-seq written 4.3 years ago by Anil Kesarwani80 • updated 4.3 years ago by Antonio R. Franco4.1k
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Comment: C: DEXSeq missing mate encountered
... The easy way could be to convert BAM to SAM and then perform awk function ...
written 4.3 years ago by Anil Kesarwani80
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Comment: C: DEXSeq missing mate encountered
... Thanks a lot for you suggestion. Can awk function work with bam (binary) ...
written 4.3 years ago by Anil Kesarwani80
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DEXSeq missing mate encountered
... Hi, I have BAM files for pairs-end reads aligned using TopHat2. The BAM files were sorted based on read name using samtools –n. But when I performed read count analysis, I found almost all reads to have missing mates. Below is the error message:   /.local/lib/python2.7/site-packages/HTSeq-0.6.1-py2 ...
tools rna-seq written 4.3 years ago by Anil Kesarwani80 • updated 4.3 years ago by Devon Ryan91k
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DEXSeq memory issue
... Hi, I am using DEXSeq v1.12 on R 3.1.1 to perfom analysis with total 573267 exons for their diffrential usage between 5 healthy and 8 patient samples (each  ~10 GB BAM file from TopHat). The job is termintated as memory exceeds the limit (~270 GB RAM). Is there any way to handle scalability of DEX ...
dexseq rna-seq written 4.3 years ago by Anil Kesarwani80 • updated 4.3 years ago by Devon Ryan91k
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Comment: C: Differential quantification of splice junction
... To me, the implementaiton of DEXSeq to calculate differential splice junction usage is not straightforward. Could you please explain me in more detail. I managed to prepare my read count (for splice junctions) file in the format of DEXSeq, but I am not able to figure out how the corresponding GTF fi ...
written 4.4 years ago by Anil Kesarwani80

Latest awards to Anil Kesarwani

Popular Question 3.2 years ago, created a question with more than 1,000 views. For How to count novel and known splice junction reads from BAM
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How does the insert size parameter change after trimming (MATS tool)
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How does MISO quantify genes with single isoform
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Extraction of splicing events and their quantification
Popular Question 3.2 years ago, created a question with more than 1,000 views. For rMATS: quantification of differential splicing
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How does the insert size parameter change after trimming (MATS tool)
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How does the insert size parameter change after trimming (MATS tool)

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