User: sjbasu

gravatar for sjbasu
sjbasu20
Reputation:
20
Status:
New User
Location:
India
Last seen:
9 hours ago
Joined:
3 years, 3 months ago
Email:
o**********@gmail.com

Posts by sjbasu

<prev • 32 results • page 1 of 4 • next >
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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 25 days ago by sjbasu20
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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 29 days ago by sjbasu20
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Comment: C: Low reads mapping in methylation sequencing
... Hello Chris, I followed your advice and used Bismark (in Bowtie1 mode) and the mapping percentage dropped even more at 3%. Is it that the methylated-Cytosines (C) are converted to thymine (T) in the methylated DNA extracted and hence the sequenced read is also having T whereas in reference genome ...
written 7 months ago by sjbasu20
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Low reads mapping in methylation sequencing
... Hello People, I have four methylation samples (MeDIP-seq) of two related plant species, testing methylation in case of saline stress. details are as follows: Sample 1: Species 1 no stress Sample 2: Species 1 with saline stress Sample 3: Species 2 no stress Sample 4: Species 2 with saline stress ...
medip mapping written 7 months ago by sjbasu20 • updated 7 months ago by Chris Miller19k
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Calculating the gene coverage in StringTie
... Hello People, I ran the new tuxedo pipeline for a reference based transcriptome analysis on HumanGenome19. After running HISAT2, I executed StringTie with -A option and got the abundance file and it looks like the following Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM ENSG00000 ...
gene stringtie coverage rna-seq written 7 months ago by sjbasu20 • updated 27 days ago by geo.pertea60
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Comment: C: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
... Hello [ole.tange][1] In case of blast, I was wondering what is the difference between using -num_threads and using parallel because when when I use parallel and do top it shows all processes are blast but cpu% is at 99-100 while I use -num_threads it shows only one process is blast but the cpu% is ...
written 7 months ago by sjbasu20
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KEGG Ontology terms depiction/statistics
... Hello People, I have a question regarding the statistics depicted in KEGG ontology term depiction. When I annotate assembled transcripts in RNA-seq experiment or predicted genes in Meta-genomic experiments, I often do pathway annotation with KEGG IDs (i.e, KO terms). Now when we give the statistic ...
kegg pathway metatranscriptome ko term rna-seq written 10 months ago by sjbasu20 • updated 10 months ago by Jean-Karim Heriche14k
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discrepancy in two known miRNA results in miRDeep2
... Hello people, I ran miRDeep2 program on a plant small rna data. After inspecting the outputs I found there are two output file with regard to known miRNA found in the data first is *result_29_01_2017_t_18_17_09.csv* second is *miRNAs_expressed_all_samples_29_01_2017_t_18_17_09.csv* ...After going t ...
rna-seq mirdeep2 mirna written 12 months ago by sjbasu20
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Comment: C: Phylogenetic analysis and Substitution rate calculation
... @Joseph Hughes..Thank you sir...clear instruction, very helpful !!! ...
written 14 months ago by sjbasu20
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Phylogenetic analysis and Substitution rate calculation
... Hello people, I have to calculate KaKs ratio. Here is what I have: 1. Assembled transcripts (using trinity) 2. 100 genes sequences of a specific gene family 3. 80 protein sequences from the before mentioned genes. Q1: How do I make the dataset for phylogenetic tree ? Should I mix the 1. (of course ...
substitution phylogenetic dnds kaks written 14 months ago by sjbasu20 • updated 14 months ago by Joseph Hughes2.5k

Latest awards to sjbasu

Popular Question 5 months ago, created a question with more than 1,000 views. For PBJelly error at mapping level
Popular Question 5 months ago, created a question with more than 1,000 views. For Gap-filling and scaffolding using PacBio reads
Popular Question 20 months ago, created a question with more than 1,000 views. For miRDeep2: expression reads and input reads not tallying

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