User: Javad

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Javad0
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Posts by Javad

<prev • 32 results • page 1 of 4 • next >
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Comment: C: How to run cutadapt in parallel
... I ran this one for example: > parallel -k -j 24 cutadapt -u 15 -o output.fastq input.fastq What can I change to make it right? Thanks a lot... ...
written 24 days ago by Javad0
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How to run cutadapt in parallel
... Hi everybody, I am using cutadapt to trim and QC of my NGS data but it is damn slow. I have also installed GNU Parallel to run it in parallel but I couldn't. To be honest, the tutorial of GNU Parallel is so complicated and I couldn't figure out how to run cutadapt in parallel with it. let's assume ...
rna-seq written 24 days ago by Javad0
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Genome annotation of mouse that only includes long non coding RNa
... Hello every body, I am working with RNA seq data that is coming from mouse. I am interested only in long non-coding RNA genes in mouse but I can not find an annotation file that only includes long non coding RNAs. Can anybody sugges a link or address that I can use to find this type of annotation f ...
rna-seq written 11 weeks ago by Javad0 • updated 11 weeks ago by GenoMax42k
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Comment: C: htseq-count output file
... Thanks a lot. It was really helpful :) ...
written 12 weeks ago by Javad0
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htseq-count output file
... Hi everybody I am trying to use htseq for counting the number of reads aligned to genomic features. I use the following command: htseq-count -s no -t exon -i gene_id --additional-attr=gene_name Alignment-files annotation-files After running the command the read count table is printed on the termi ...
rna-seq written 12 weeks ago by Javad0 • updated 12 weeks ago by michael.ante2.2k
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Comment: C: single cell RNA-seq 10X genomics
... This paper is a good start to understand differences between single cell rna seq and bulk rna seq analysis. Stegle, Oliver, Sarah A. Teichmann, and John C. Marioni. "Computational and analytical challenges in single-cell transcriptomics." Nature Reviews Genetics 16.3 (2015): 133-145. ...
written 3 months ago by Javad0
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How to import read count matrix into CellDataSet object
... Dear all, I get stuck with something basic. I have a read count table (a matrix) and I want to import it into [monocle][1]. What is the format of feature data and pheno data that I need to use and what is the format of data matrix ? Thanks a lot [1]: http://cole-trapnell-lab.github.io/monocle- ...
rna-seq written 3 months ago by Javad0 • updated 3 months ago by Pierre Lindenbaum104k
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Comment: C: How I can produce graphs like this
... It is just a gene expression. I need to show the percentage of each gene in diffrerent group. each colour here represents a gene and the height of column represents the percentage of gene expression. ...
written 3 months ago by Javad0
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How I can produce graphs like this
... Hello every body, Could you please tell me which R package can I use to produce graphs like this? Thanks in advance. ![enter image description here][1] https://ibb.co/fTZMAm [1]: https://image.ibb.co/cW6CGR/Screenshot_from_2017_10_26_14_09_23.png ...
next-gen rna-seq written 3 months ago by Javad0 • updated 3 months ago by Sreeraj Thamban80
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Comment: C: How to run a Perl script
... Thanks, But how I can define the input and output file? ...
written 4 months ago by Javad0

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Supporter 23 days ago, voted at least 25 times.

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