User: Javad

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Javad120
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3 years, 6 months ago
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Posts by Javad

<prev • 53 results • page 1 of 6 • next >
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How to count the number of reads aligned to rRNA
... Dear all, I am working on an organism that has 10 copies of rRNA genes on its genome. I would like to see the percentage of reads that are aligned to ribosomal RNA. After alignment, rRNA reads align to every and each of these genes and if I perform the counting for reads that are not uniquely alig ...
rna-seq written 12 weeks ago by Javad120
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Comment: C: problem installing cutadapt
... Hi, As I said above, conda doesn't help. It leads to the same error. ...
written 8 months ago by Javad120
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Comment: C: problem installing cutadapt
... Hi. Python 3.7.4 ...
written 8 months ago by Javad120
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problem installing cutadapt
... Dear all, I have difficulty installing cutadapt on my system. After installing cutadapt with `pip3 install --user --upgrade cutadapt` and running `cutadapt --version`, I get the following error that don't know how to address it. Traceback (most recent call last): File "./cutadapt", line ...
rna-seq written 8 months ago by Javad120 • updated 8 months ago by Ido Tamir5.1k
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How to separate different kinds of RNA in my list of gene
... Dear all, I have a normal RNA seq count table with around 40000 rows. In my data I would like to seperate "protein coding", long non-coding", "pseudo gene", "misc" RNA etc. to analyse each one of them separately. (I have the Ensemble ID corresponding to each row). is there a straight forward way to ...
rna-seq written 18 months ago by Javad120
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How to create a back-end database of gene expression data
... Dear all, I have a question regarding database management. I would be really grateful if somebody here can help me. I have a table with 100,000 columns and 30,000 rows that I would like to store it in a back end database like SQLite or mySQL. The problem is that programs like SQLite have a limitati ...
rna-seq written 19 months ago by Javad120
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Differential expression analysis of normalized expression of RNA seq data
... Dear All, I have a normalized expression table of RNA seq data. I normally use DESeq2 but it needs raw count table not normalized data. Which R package I can use to analyse a Normalised table? Best, ...
rna-seq written 2.2 years ago by Javad120 • updated 2.2 years ago by Benn8.0k
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Comment: C: How to count different features at the same time with htseq
... Then how the command would look like? ...
written 2.2 years ago by Javad120
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How to count different features at the same time with htseq
... Dear all, I want to do counting of my data set and I do like to count the number of reads aligned to the gene, UTR and sRNA at the same time. As the --type argument of htseq only accepts one feature at a time, is there a way that I can count these features together. And if this is not possible wi ...
rna-seq written 2.2 years ago by Javad120
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Comment: C: how to produce plots like this in R
... Thanks a lot. It is a very good suggestion but the problem is that I need something that I have full control on the graph production. I need to factor the data and compare different data sets in a same figure. That is why I asked for a ggplot2 tutorial. ...
written 2.3 years ago by Javad120

Latest awards to Javad

Popular Question 7 months ago, created a question with more than 1,000 views. For Tools for Saturation analysis and gene body coverage analysis
Popular Question 7 months ago, created a question with more than 1,000 views. For Demultiplexing bcl files into fastq files
Popular Question 7 months ago, created a question with more than 1,000 views. For The best way to produce gene body coverage
Popular Question 7 months ago, created a question with more than 1,000 views. For Combining several fasta files and gff files
Popular Question 7 months ago, created a question with more than 1,000 views. For Differential expression analysis of normalized expression of RNA seq data
Popular Question 8 months ago, created a question with more than 1,000 views. For The best way to produce gene body coverage
Great Question 16 months ago, created a question with more than 5,000 views. For looking for an R package for GO term analysis
Epic Question 16 months ago, created a question with more than 10,000 views. For looking for an R package for GO term analysis
Popular Question 16 months ago, created a question with more than 1,000 views. For The best way to produce gene body coverage
Popular Question 16 months ago, created a question with more than 1,000 views. For SNPs in 1000 genome project
Popular Question 16 months ago, created a question with more than 1,000 views. For Converting different annotation file formats (GTF/GFF/BED) to each other
Popular Question 16 months ago, created a question with more than 1,000 views. For Demultiplexing bcl files into fastq files
Popular Question 16 months ago, created a question with more than 1,000 views. For Converting GTF file to UCSC-styled bed file
Student 16 months ago, asked a question with at least 3 up-votes. For how to produce plots like this in R
Popular Question 17 months ago, created a question with more than 1,000 views. For Converting GTF file to UCSC-styled bed file
Popular Question 19 months ago, created a question with more than 1,000 views. For Converting GTF file to UCSC-styled bed file
Popular Question 19 months ago, created a question with more than 1,000 views. For How to manipulate a gff or gtf file manually?
Popular Question 21 months ago, created a question with more than 1,000 views. For Converting GTF file to UCSC-styled bed file
Popular Question 21 months ago, created a question with more than 1,000 views. For Converting GTF file to UCSC-styled bed file
Great Question 23 months ago, created a question with more than 5,000 views. For looking for an R package for GO term analysis
Popular Question 23 months ago, created a question with more than 1,000 views. For Converting GTF file to UCSC-styled bed file
Popular Question 23 months ago, created a question with more than 1,000 views. For looking for an R package for GO term analysis
Popular Question 23 months ago, created a question with more than 1,000 views. For RNA spike-ins: Their applications and bioinformatics methods for the analysis
Popular Question 2.2 years ago, created a question with more than 1,000 views. For htseq-count output file
Popular Question 2.2 years ago, created a question with more than 1,000 views. For htseq-count output file

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