User: nabiyogesh

gravatar for nabiyogesh
nabiyogesh80
Reputation:
80
Status:
Trusted
Location:
South Korea
Last seen:
1 week, 4 days ago
Joined:
11 months, 4 weeks ago
Email:
n*********@gmail.com

Posts by nabiyogesh

<prev • 200 results • page 1 of 20 • next >
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Comment: C: Error building database in snpEff
... Please make a folder like (mm37.61) in this path: /home/path/snpEff/data/mm37.61 put fasta and gtf file there and then in config file mention these file like this: data_dir = /home/path/snpEff/data/mm37.61 I hope this may help you. ...
written 4 months ago by nabiyogesh80
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coding potential tool for de novo assembled transcripts for plant species
... Is there any other tool than CPC for calculation of coding potential for de novo assembled transcripts for plant species whose genome sequences is not available. Thanks Yogesh ...
rna-seq written 4 months ago by nabiyogesh80 • updated 4 months ago by haro200
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Comment: C: How to extract equal number of R1 and R2 read from raw Illumina data
... Thanks a lot. with this command, it is coming correct number: awk '{s++}END{print s/4}' fastq file name Thanks again! ...
written 5 months ago by nabiyogesh80
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How to extract equal number of R1 and R2 read from raw Illumina data
... Dear All, Somehow, We got different number of R1 and R2 reads in Illumina paired end sequencing data. Is there any way to extract equal number of R1 and R2 reads from these raw files. these are just pair end library not strand specific. [root@psgl data_new]# grep -c '^@' SS_5W_R1.fastq ...
rna-seq written 5 months ago by nabiyogesh80 • updated 4 months ago by st.ph.n1.9k
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Comment: C: Find number of rows contain zero raw count across all sample (column) using R
... Thanks a lot for encouraging comment especially WouterDeCoster. I do not take his advise as a negative sense because I am in learning stage and really we learn thing better way when we try to resolve problem by ourself, but sometime help is also needed. > dim(countMatrix) [1] 57894 33 ...
written 5 months ago by nabiyogesh80
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Comment: C: Deseq2 pairwise comparision
... Thanks a lot for helping me. I read sampleinfo (colData) as a csv file like this: SampleInfo<- read.csv("sampleInfo.csv", check.names=F) I need to ask you one thing about biological replicate information. 216_5W_Ca1 and 216_5W_Ca2 are biological replicate.... How should I add information abou ...
written 5 months ago by nabiyogesh80
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Comment: C: Deseq2 pairwise comparision
... I tried to type all condition on linux platform itself but again getting ERROR: > colData <- data.frame(genotypes = c('216','216','216','216','216','216','216','216','216','216','216','216','216','216','216','216','218','218','218','218','218','218','218','218','218','218','218','218','21 ...
written 5 months ago by nabiyogesh80
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Comment: C: Deseq2 pairwise comparision
... I tried to make ColData like this: ColData <- data.frame (genotypes = c(‘216’, ‘216’, ‘216’, ‘216’, ‘216’, ‘216’, ‘216’, ‘216’, ‘216’, ‘216’, ‘216’, ‘216’, ‘216’, ‘216’, ‘216’, ‘216’, ‘218’, ‘218’, ‘218’, ‘218’, ‘218’, ‘218’, ‘218’, ‘218’, ‘218’, ‘218’, ‘218’, ‘218’, ‘218’, ‘218’, ‘218’, ...
written 5 months ago by nabiyogesh80
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Comment: C: Deseq2 pairwise comparision
... Thanks I read DESeq2 Vignette, but I am not able to understand.. what do you mean by pair end samples.....is it about lines like I have 216 and 218? I am not able to understand multi factor designs. How do I make colData and desing formula in above command? ...
written 5 months ago by nabiyogesh80
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Deseq2 pairwise comparision
... There are two line 216 and 218 Three development stages 5 WEEK (5W), 7W, 9W. Three tissue: Ca, Co, Pa each with 2 biological replicate. With two biological replicate. I want to do differential gene expression analysis using DESeq2 so I tried these codes after reading about DESeq2: ,my aim is to ...
rna-seq written 5 months ago by nabiyogesh80 • updated 5 months ago by dr_bantz50

Latest awards to nabiyogesh

Popular Question 19 days ago, created a question with more than 1,000 views. For how to extract pair end reads from bam file using samtool
Popular Question 8 weeks ago, created a question with more than 1,000 views. For how to extract pair end reads from bam file using samtool
Popular Question 8 weeks ago, created a question with more than 1,000 views. For How to extract unmapped Paired end reads from BWA output sam file
Popular Question 8 weeks ago, created a question with more than 1,000 views. For How to install Trimmomatic-0.36
Popular Question 5 months ago, created a question with more than 1,000 views. For How to install Trimmomatic-0.36
Centurion 8 months ago, created 100 posts.
Supporter 10 months ago, voted at least 25 times.
Rising Star 10 months ago, created 50 posts within first three months of joining.

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