User: sjbasu

gravatar for sjbasu
sjbasu30
Reputation:
30
Status:
New User
Location:
India
Last seen:
3 months, 2 weeks ago
Joined:
3 years, 10 months ago
Email:
o**********@gmail.com

Posts by sjbasu

<prev • 34 results • page 1 of 4 • next >
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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 6 months ago by sjbasu30
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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 6 months ago by sjbasu30
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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 7 months ago by sjbasu30
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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 8 months ago by sjbasu30
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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 14 months ago by sjbasu30
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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 14 months ago by sjbasu30 • updated 14 months ago by Chris Miller20k
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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 14 months ago by sjbasu30 • updated 7 months 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 14 months ago by sjbasu30
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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 17 months ago by sjbasu30 • updated 17 months ago by Jean-Karim Heriche16k
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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 20 months ago by sjbasu30

Latest awards to sjbasu

Popular Question 12 months ago, created a question with more than 1,000 views. For PBJelly error at mapping level
Popular Question 12 months ago, created a question with more than 1,000 views. For Gap-filling and scaffolding using PacBio reads
Popular Question 2.2 years ago, created a question with more than 1,000 views. For miRDeep2: expression reads and input reads not tallying

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