User: BioBing

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BioBing50
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Posts by BioBing

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Diamond annotation versus Kallisto/Sleuth
... Thank you! I am waiting for Trinotate to be configurated on the cluster I am using, that is why I have been using Diamond ...
written 4 weeks ago by BioBing50
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Diamond annotation versus Kallisto/Sleuth
... Hi all Annotation Experts out there, Currently, I am working with differential gene expression in a non-model organism. For this, I have used Kallisto/Sleuth and is very pleased with the process as well as the results. But **I am stuck** and would be really grateful for some help to move on. My ...
R rna-seq blast sequencing written 5 weeks ago by BioBing50
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Modifications of graphs from Sleuth Object?
... Dear Biostar users, I have been using Kallisto/Sleuth to analyze my RNA-seq data and have a couple of questions related to the modification of heat maps based on a sleuth object (so), that I hope someone can help me with: **Question 1:** I am a bit puzzled about what the "value" that goes from 0-6 ...
R rna-seq written 9 weeks ago by BioBing50
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Answer: A: Trimmomatic - unknown trimmer?
... I solved it! By deleting -trimlog, -inbase and -outbase - as well as found a space that should not be there, it worked! In case others have the same issue, this is how my code looked like: Trimmomatic PE L001_R1.fastq L001_R2.fastq out_L001_R1_P.fastq out_L001_R1_U.fastq out_L001_R2_P.fastq L ...
written 12 weeks ago by BioBing50
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Trimmomatic - unknown trimmer?
... Hi all, I am really struggling with Trimmomatic these days and the frustration level is rising (I have to meet a deadline). For multiple days Trimmomatic, on usegalaxy.org, has given me an error as soon as I apply the IlluminaClip: > Fatal error: Exit code 1 () Trimmomatic did not finish succe ...
software error sequence next-gen rna-seq written 12 weeks ago by BioBing50
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Comment: C: BUSCO - issue reading the fasta file
... Thank you :-) I solved it, I had forgotten to define the paired end reads! ...
written 3 months ago by BioBing50
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Comment: C: Normalization of RNAseq data and the use of de novo transcriptome
... Ops, I meant E90N50 :-) Thank you! I have considered kallisto as well ...
written 3 months ago by BioBing50
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Answer: A: transcriptome assembly evaluation
... You can also run a BUSCO analysis on the two assemblies (to test the "completeness"): http://busco.ezlab.org/ I like Detonate (suggested by Carlos Caucedo) to compare my transcriptome assemblies :-) ...
written 3 months ago by BioBing50
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Normalization of RNAseq data and the use of de novo transcriptome
... Hi all, Hoping that some of the RNAseq experts in here are having some pieces of advice on normalization/proceeding of following data analysis: The study is about how a stressor is affecting a non-model species (no reference genome/transcriptome available) in terms of differential gene expression. ...
dge rna-seq denovo transcriptome written 3 months ago by BioBing50 • updated 11 weeks ago by theobroma22570
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Is it possible to retrieve data from a Detonate run?
... Dear DETONATE experts, I need your help! The last couple of days, my computer have been running DETONATE non-stop to compare two transcriptome assemblies (very deep sequencing - so it takes forever). When I came back from a coffee break, I realized something terrible; I had forgotten to turn off ...
assembly next-gen rna-seq detonate sequencing written 3 months ago by BioBing50

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