User: sjbasu

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Posts by sjbasu

<prev • 30 results • page 1 of 3 • next >
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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 days ago by sjbasu0
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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 8 days ago by sjbasu0 • updated 8 days ago by Chris Miller18k
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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 10 days ago by sjbasu0
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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 21 days ago by sjbasu0
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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 3 months ago by sjbasu0 • updated 3 months ago by Jean-Karim Heriche12k
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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 5 months ago by sjbasu0
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Comment: C: Phylogenetic analysis and Substitution rate calculation
... @Joseph Hughes..Thank you sir...clear instruction, very helpful !!! ...
written 7 months ago by sjbasu0
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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 7 months ago by sjbasu0 • updated 7 months ago by Joseph Hughes2.1k
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Gap-filling and scaffolding using PacBio reads
... Hello people, Has anyone in here used OPERA-LG or PBJelly to improve assembly by better scaffolding and filling in gaps ? Actually I am seeking explanation to few "abnormalities" that I am not able to understand: 1. After running OPERA-LG (Paired end data + pacbio data), the max scaffold size inc ...
genome assembly opera-lg pbjelly pacbio written 9 months ago by sjbasu0 • updated 10 weeks ago by ant_genome0
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OPERA-LG error: short reads are not mapping
... Hello people, I am using OPERA-LG on bacterial genomic data (more like a test run before I use it on actual mammalian genome) from illumina (short reads) and pacbio (long reads). The short reads were used to generate contigs using velvet. Now when I am executing the OPERA-long-read.pl script on my ...
assembly opera-lg scaffolding written 10 months ago by sjbasu0

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Popular Question 13 months ago, created a question with more than 1,000 views. For miRDeep2: expression reads and input reads not tallying

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