User: Light92

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Light9220
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Location:
Italy
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3 months, 1 week ago
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1 year, 2 months ago
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Posts by Light92

<prev • 30 results • page 1 of 3 • next >
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How to analyze RNA Targeted (Gene Panel) Ampliseq data?
... Good evening to anyone, I'm about to get the results of my experiment. A panel of selected genes of insterest (250) have been successfully analyzed through different tissues by using a RNA Targeted approach, provided by Illumina Ampliseq. I don't have any of the default tools suggested on the websit ...
ampliseq panel rna targeted amplicons written 3 months ago by Light9220
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Comment: C: Trobules using R function goana to perform GO enrichment analysis
... Hello, thanks for your answer! Sadly, it doesn't seem to be the case. In the past, I used the function goana (with a mild change in the code) to acquire an external given database, not online ones, and it worked perfectly... The problem seems to be something different since, as I explained in the to ...
written 5 months ago by Light9220
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Comment: C: Performing GO enrichment analyis on DE genes
... This is similar to what I wanted to do in case there is no alternative. More specifically, I'm working on domesticated olive tree and I could try by blasting domestic olive tree genes against *Olea europaea var. sylvestris* ones, so that I could use the GO annotations of the latter once I know the c ...
written 5 months ago by Light9220
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Performing GO enrichment analyis on DE genes
... Good morning to everyone, To complete a DE genes analysis, at the end of my pipeline (during which I adopted DESEQ2 and edgeR methods, to compare results), I'd like to perform a GO enrichment analysis. My main problem is that the GO terms aren't available on databases online, since I'm using a gen ...
rnaseq enrichment de go written 5 months ago by Light9220
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Trobules using R function goana to perform GO enrichment analysis
... Good morning to everyone, I'm trying to use the function goana to run a GO enrichment analysis after performing the workflow [RnaSeqGeneEdgeRQL][1]. I obtained a list of DE genes with the function glmQLFTest (on the left), and shortly after I decided to use glmTreat as well (on the right), to obtain ...
rnaseq R bioconductor de go written 5 months ago by Light9220 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: Trimmomatic parameters for Trinity transcriptome assembling
... I see! So I guess SLIDINGWINDOW is a more accurate approach! Thank you! ...
written 6 months ago by Light9220
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Comment: C: Trimmomatic parameters for Trinity transcriptome assembling
... > and then there is a syntax error as it should read LEADING:25 > TRAILING:25 (no spaces, with colon) Thanks for pointing this out, you're right (and Trimmomatic noticed me after a while by showing a NumberFormatException in the log...) > I would rather go for the slidingwindow one (in st ...
written 6 months ago by Light9220
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Comment: C: min_contig_length parameter in Trinity - Isoforms discrimination
... I see, thanks! But I was wondering since I saw different choices in scientific papers what it affects apart from noise? ...
written 6 months ago by Light9220
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Comment: C: Trimmomatic parameters for Trinity transcriptome assembling
... I would suggest to run the trimmomatic step separate from the trinity step as this will give you more control and insight what is going on. Good suggestion, even though Trimmomatic is launched before Trinity assembling starts and it even produces .gz compressed reads you can use separately... ...
written 6 months ago by Light9220
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min_contig_length parameter in Trinity - Isoforms discrimination
... Good morning to everyone, I'm trying to build a reference transcriptome from different plant tissues (root, leaf, bud, flower etc), with paired-end Illumina TruSeq reads. I was wondering... how about the Trinity parameter min_contig_length? I set a 300 but I've read online it really depends on th ...
assembly transcriptome trinity written 6 months ago by Light9220

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Scholar 14 months ago, created an answer that has been accepted. For A: mpiblast returning an error with a specific FASTA file - Unable to open files

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