User: Javad

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Javad0
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Posts by Javad

<prev • 18 results • page 1 of 2 • next >
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Tools for Saturation analysis and gene body coverage analysis
... Hello, I have a set of RNA-seq data and I want to perform saturation analysis and gene body coverage analysis on them. Which tools can I use for this type of analysis? Thanks ...
rna-seq written 4 days ago by Javad0
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Comment: C: Converting different annotation file formats (GTF/GFF/BED) to each other
... Thanks It was very helpful. ...
written 6 days ago by Javad0
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Converting different annotation file formats (GTF/GFF/BED) to each other
... Hello everybody, What is the most efficient way to convert different annotation file formats to each other. GFF --> GTF GTF --> BED Thanks in advance. ...
next-gen rna-seq written 6 days ago by Javad0
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How to manipulate a gff or gtf file manually?
... Hello, I want to manipulate a gtf file manually. I can do this with text editors like gedit. It works very well with small genomes like bacterial genomes but when it comes to big genomes (like human genome) It is slow and it needs high amount of memory to load the annotation file. Is there another ...
genome next-gen rna-seq written 7 days ago by Javad0 • updated 7 days ago by shoujun.gu220
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Comment: C: Normalization of RNA-seq data
... Thanks for your answer. My libraries are sequenced deep enough and I have sufficient number of reads that are aligned to mRNAs. Of course around 90 percent of my reads are aligned to rRNA but I still have around 2 or 3 million reads that are uniquly aligned to mRNAs and I think this amount is suffic ...
written 11 days ago by Javad0
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Normalization of RNA-seq data
... Hello, I have few libraries that are not rRNA depleted and in each of them we have high percentage of reads that are aligned to rRNA genes. I want to normalize data in order to perform multiple comparisons to find differentially expressed genes. My question is that if I normalize data with method ...
rna-seq written 12 days ago by Javad0 • updated 12 days ago by Satyajeet Khare1.0k
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where to download ERCC RNA spike ins fasta and gff file?
... Hi everyone, Could you please tell me where I can find the annotation and fasta file related to ERCC 92 spike ins. The Thermo fisher website only gives the fasta file. Is there any other link that I can download compatible fasta and gff files? Thanks a lot ...
rna-seq written 12 days ago by Javad0 • updated 12 days ago by Devon Ryan70k
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Combining several fasta files and gff files
... Hello, I have several fasta formatted files which I need to combine them. In addition I have few gff formatted files that I need to combine too. Which tool can I use to do the combination Thanks in advance ...
rna-seq written 13 days ago by Javad0
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Comment: C: RNA spike-ins: Their applications and bioinformatics methods for the analysis
... Thanks for your response. Actually my data set is a single cell RNA seq data. ...
written 13 days ago by Javad0
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RNA spike-ins: Their applications and bioinformatics methods for the analysis
... Hello, I have a few RNA-seq data which is mixed with ERCC spike-ins. I want to convert the read counts to transcript counts using these ERCC spike-ins. Unfortunately I can not find a good reference which explains how ERCCs work and how they can be used for this type of conversion. I would be gratef ...
rna-seq written 13 days ago by Javad0

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