Hi all!
I have generated genome assemblies for my samples and would like to find the location of coding sequences in the contigs. Using coding...
129 results in 0.0036 seconds.
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Command line BLAST to identify genes in genome assemblies
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Estimate cell label fitness in a clustering
Dear fellows –
I have a task to overlay the “good and known” single-cell annotations on the newly generated PC matrix (or its corresponding... -
training GeneMark for gene prediction
Hi,
I'm want to annotate a big, complex eukaryotic genome from non-model using GeneMark 4.69 gene prediction.
I want to train... -
Job - Senior Software Developer / Bioinformatician (Genome Annotation and Analysis)
Applications are invited for a Senior Software Developer/Bioinformatician to join the Core Bioinformatics Group at the Earlham Institute (EI), based in... -
Extracting gene sequences from Stringtie assembly
Hi all,
Forgive me if this question has been posted before (I'm new to this forum). In the past, when doing transcript-level RNA-seq analyses,... -
Minimum transcriptome requirement for genome annotation
Hi,
I would like to know if there is any information available on the minimum number of transcriptomes required to get a genome annotation... -
Pfam search using hmmer but only for a specific taxonomy
I am trying to do a de novo assembly using Trinity. Using Transdecoder and blastp/hmmscan search to do annotation (using Uniprot/pfam databases). htt... -
Maker AWS AMI
Anyone know where where I can find an already set up AWS AMI for running the Maker pipeline?
Thanks! -
Strand information in DMR identification and annotation
Hello,
Does anyone have any information/advice on whether strand information from aligned reads is taken into account during the identification... -
Background for GO term enrichment analysis of RRBS DMR data?
Hi,
I am attempting to carry out GO term enrichment analysis on set of differentially methylated genomic regions (DMRs). The program I am... -
What's the exact pathway to handle paired end fastq data so you finally make it into
I've unmapped cleaned paired end sequence data in fastq format of a bacterial genome. I want to get a sequence data in Genbank format in the end. What's... -
Adding Blastx Hits to un-identified genes in StringTie Output
Hi all,
I've been using a general pipeline of Hisat2 -> StringTie -> Ballgown for differential gene expression analysis in a non-model... -
Protein annotation parameters (query or subject coverage?)
Hi there.
I am annotating some proteins' functions and I a have some doubts about the parameters I should use. I'm using e-value below... -
How to decide the side (5' or 3') close to TSS in GTF
Hi everybody
I’d like to ask you about TSS (transcription start site) annotation
Now I’m analyzing Total RNA-seq data by ENCODE... -
Reconstruction method of repeatMasker output
Hi everyone
I'd like to ask you about reconstruction method of repeatMasker output.
These days, I started my new research project...
