Hello everyone,
I am trying to analyze my bulk RNAseq data set from hippocampal tissue extracted from our WT/KO mice. The knockout consists...
13 results in 0.0028 seconds.
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GTF/Reference genome adjustments? Gene-based differential expression analysis of genetically modified mouse line
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Help with ERV analysis
Hi,
Very new to this! Apologies if not enough information given.
I'm trying to count the change in ERV expression before and after treatment...Last edited by icd20; 02-08-2021, 07:53 AM. -
How to align raw data to custom regions of the genome?
I have a bed file of some custom regions I have interest in, e.g.
chr1 1000 1015 my_region 0 +
...
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TopHat v2.1.1- Warning: TopHat did not find any junctions in GTF file
I'm running TopHat v2.1.1 on Mycobacterium tuberculosis genome using the gtf file download from the EnsemblBacteria FTP. When trying map to genome I get... -
GFF3 files for small RNA
Hi everyone,
I'm looking for gtf/gff/gff3 files for small RNA (sequencing run based on a MiSeq with small RNA kit). Does anyone know where to get... -
How to clean the GTF file downloaded from Ensembl
Hi, all
Recently, I have downloaded a GTF file from Ensembl and found that there're coding and non-coding transcript annotations in the... -
featureCounts error
Hi,
I have a problem with featureCounts gtf file.
I want to count the miRNA reads using the sorted .bam file containing... -
Cuffcompare: difference between "nearest_ref" and "oID"
Hello Everyone,
I am a master student new to cufflinks and i am using cuffcompare in order to evaluate an overall analysis on the same... -
DESeq - need FASTA and GTF from same resource
I am following the DESeq protocol.
It suggests for me to download a reference genome sequence for the organism under study (homo sapiens)... -
How to annotate genes from gene prediction
Hi,
For a completly novel genome I used a gene prediction software called SNAP (http://korflab.ucdavis.edu/software.html) and it provided me a GFF...Last edited by mictadlo; 09-17-2013, 06:00 PM. -
appropriate gtf/gff file for repeat element expression
Dear Folks,
I am trying to estimate the expression of known repetitive elements.
I'd like to know what'd be an appropriate... -
Drosophila Annotation Files
Hello,
I have been working with a couple different Drosophila annotation files for an RNAseq experiment. I was wondering if within the... -
GTF difference in CDS and exon start position
Hi all,
I have a question about the annotation of features in some GTF files. So basically, I've seen that quite often the CDS and exon...
