User: SJ Basu

gravatar for SJ Basu
SJ Basu30
Reputation:
30
Status:
New User
Location:
India
Last seen:
2 weeks, 3 days ago
Joined:
5 years, 2 months ago
Email:
o**********@gmail.com

Computatinal biologist at Tata Translational Cancer Research Center. I work on NGS data of mainly leukemia samples for translational research. I believe communication, collaboration and perseverance is how you progress in science. 

Posts by SJ Basu

<prev • 40 results • page 1 of 4 • next >
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Processing RNA-seq expression for inter sample classification
... Hello People, With a hope not to complicate this post beyond comprehensibility, I would like to seek help on two related operations regarding an RNASeq experiment that I recently performed. I have a set of 25 samples (leukemia) that were sequenced using whole RNA kit on illumina platform. I have a ...
stringtie classification rna-seq dge written 8 months ago by SJ Basu30
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Comment: C: Too low FPKM values from StringTie
... Hi Kevin, Thanks for reassurance and the information. As for the FPKM units, so which units can reliably be used for differential expression comparisons ?? TPM ?? ...
written 11 months ago by SJ Basu30
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Comment: C: Too low FPKM values from StringTie
... Actually the problem is I don't see a "CURVE", its just a really long, sharp PEAK at ~0 FPKM value....it looks I might as well take a cut-off of FPKM value of 2 and still would retain more than 25K genes. Another thing is, which FPKM do you consider ? The one that is given by -A option or the one t ...
written 11 months ago by SJ Basu30
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Comment: C: Too low FPKM values from StringTie
... Hi Shawn, These are WBCs (leukemia) extracted from FFPE samples but rna quality was good. For number of genes >0 is ~35k , >1 is ~15-18k and >10 is ~3-5k "I'm wondering if annotated but unexpressed genes are hiding the true signal"...I didn't exactly get that.... ...
written 11 months ago by SJ Basu30
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Too low FPKM values from StringTie
... Hello People, I am analyzing 20 samples RNA-Seq data of leukemia. To this end, I have used the Hisat2-StingTie2 pipeline to analyze the samples and arrive at FPKM counts for each gene. After I have run the complete process, I found that the FPKM values are way too low for calculating Differential ...
new tuxedo stringtie rna-seq written 11 months ago by SJ Basu30
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variant calling using data from HaloPlex HS
... Hello, I have recently received HaloPlex HS data for 20 cancer samples. I was to call single nucleotide variants from the fastq reads. I have used GATK best practice pipeline to call variants and then annotate with SNPeff and annovar. But a friend of mine, suggested that HaloPlex HS reads needs to ...
agilent snp targetted sequencing haloplex hs written 16 months ago by SJ Basu30
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Answer: A: mapping rate of small rna-seq with different references
... Firstly I assume you are analysis is primarily miRNA detection. So when you map smRNA reads, they being very small sequence tends to map everywhere along the genome. Now for the anomaly in mapping %age, it can happen due to a lot of reasons like masking, incorrect chromosomal file concatenation, d ...
written 22 months ago by SJ Basu30
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characterizing a plasmid genome
... Hello People, I have a problem related to characterizing a novel plasmid genome of a coccus species bacteria. I have Illumina 2X150 sequenced reads of plasmid. The data was assembled in scaffolds. Now I realize that there can be contamination of genomic scaffolds, so I blastN the scaffolds to NT a ...
plasmid ngs plasmid genome microbiology written 22 months ago by SJ Basu30
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Comment: C: Calculating the gene coverage in StringTie
... Finally have the answer from The Author !!...Though I guessed some of these facts but was in need for confirmation...These facts answer a few other queries regarding the tool too. Thank you so much [Geo.pertea][1]. [1]: https://www.biostars.org/u/44094/ ...
written 24 months ago by SJ Basu30
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Comment: C: Calculating the gene coverage in StringTie
... Actually I have tried to look for the answer elsewhere but to no success ...and I also tried to calculate and arrive at the given results by looking at reads mapped at each bases of the shown genes in IGV and still couldn't regenerate the result values !!! ... ...
written 24 months ago by SJ Basu30

Latest awards to SJ Basu

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Retriving the base and its quality from fastq file
Popular Question 6 months ago, created a question with more than 1,000 views. For Retriving the base and its quality from fastq file
Popular Question 6 months ago, created a question with more than 1,000 views. For Gap-filling and scaffolding using PacBio reads
Popular Question 6 months ago, created a question with more than 1,000 views. For choice of reference for transcriptome assembly
Popular Question 7 months ago, created a question with more than 1,000 views. For Retriving the base and its quality from fastq file
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 15 months ago, created a question with more than 1,000 views. For Retriving the base and its quality from fastq file
Popular Question 15 months ago, created a question with more than 1,000 views. For Jellyfish for transcriptome assembly
Popular Question 19 months ago, created a question with more than 1,000 views. For PBJelly error at mapping level
Popular Question 2.4 years ago, created a question with more than 1,000 views. For PBJelly error at mapping level
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Gap-filling and scaffolding using PacBio reads
Popular Question 3.6 years ago, created a question with more than 1,000 views. For miRDeep2: expression reads and input reads not tallying

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