User: Light92

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Light9220
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New User
Location:
Italy
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2 weeks, 4 days ago
Joined:
4 months, 2 weeks ago
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Posts by Light92

<prev • 19 results • page 1 of 2 • next >
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Comment: C: How to distinguish between 16S chloroplast reads and real bacteria ones?
... This would be greatly appreciated, thanks! However, I'm mainly interested in the primers choice. ...
written 18 days ago by Light9220
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Comment: C: How to distinguish between 16S chloroplast reads and real bacteria ones?
... Hi, thanks for your advice! I checked your paper out, but it appears not to be available for free, and the abstract just says very little. Could you expand on such methods, even through a private message? It would be greatly appreciated! Thanks in advance! ...
written 19 days ago by Light9220
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Comment: C: How to distinguish between 16S chloroplast reads and real bacteria ones?
... Thanks for the suggestion, but I wasn't referring to this. I have already tried the qiime taxa filter-table function and it works like wonder, but it just removes the reads I'm not interested on from the QIIME 2tables. The problem isn't about filtering data, but about obtaining data with a lower co ...
written 20 days ago by Light9220
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How to distinguish between 16S chloroplast reads and real bacteria ones?
... Hello, In an old experiment dating back to 2014, some 16S libraries from plant samples were prepared, with the aim to identify the microbial community living/contaminating the surface of the fruits. The primer choice was the couple 27F and 533R. Sadly, once analyzed with QIIME2 and clustered, out ...
16s qiime2 metagenomics primers sequencing written 20 days ago by Light9220 • updated 19 days ago by andres.firrincieli280
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Comment: C: How to perform KEGG enrichment analysis for DE genes from a de-novo transcriptom
... It worked like a bless! Thank you! ...
written 8 weeks ago by Light9220
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How to perform KEGG enrichment analysis for DE genes from a de-novo transcriptome?
... Hello, I'm running a pipeline to analyze differential expression for transcripts predicted and BLAST-annotated from a de-novo assembled transcriptome... At the end of the pipeline, I'm interested in a KEGG Enrichment analysis, but I have no idea about how to perform it. I used Trinity till now but ...
kegg enrichment kegg written 9 weeks ago by Light9220
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GOplot error - Gene Ontology plot generation errors
... Hello, I'm trying to run the Trinity script prepnrunGOplot.pl to get plots after GO enrichment analysis (calculated with analyzediff_expr.pl), comparing two samples previously DE analyzed. It calls the goplot package, but I'm getting errors I can't understand I ran: ./prep_n_run_GOplot.pl --G ...
trinity goplot gene ontology bioconductor written 10 weeks ago by Light9220
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Comment: C: Converting an output de-novo transcriptome assembled with Trinity to a .gff3 fil
... I've tried to use GMAP, with the following code, but the script seems to freeze for no reason and I get an empty output file. gmap -d Trinity.fasta -f 3 > meh.gff3 What do you mean by reference? It's a de-novo assembly, because my organism is not a model one, so I don't really have one. ...
written 10 weeks ago by Light9220
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Converting an output de-novo transcriptome assembled with Trinity to a .gff3 file
... Hello! I've de-novo assembled a transcriptome from Trinity, resulting into Trinity.fasta, whose headers look like this: >TRINITY_DN29256_c0_g1_i1 len=323 path=[0:0-322] Followed, in the next line, by the sequence. To run an external downstream analysis with a R script, I'd need to have a . ...
trinity written 10 weeks ago by Light9220 • updated 26 days ago by h.mon28k
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GO enrichment analysis graphs after goseq: any easy solutions?
... Hello everyone! I've performed a differential gene expression analysis through Trinity, as suggested [here][1]. GO enrichment analysis was also performed through the analyze_diff_expr.pl script. The function calls the R package **goseq**, and [as stated here][2], the output looks this way: *Two out ...
go terms gene ontology go enrichment goseq written 10 weeks ago by Light9220 • updated 10 weeks ago by Benn7.9k

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Scholar 4 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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