User: manuelmendoza

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Posts by manuelmendoza

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Comment: C: Trinity de novo assembly without reference genome (community metatranscriptome)
... I'm so sorry but I don't know how to send a personal message throw this portal... you can contact me by github: manuelsmendoza ...
written 9 months ago by manuelmendoza40
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makeTxDbFromGFF Problem - GenomicFeatures R package
... Hi! I am trying to make a TxDB using GenomicFeature R package using my gff3 file but I don't understand the error that the package thought out. Does anyone know what is happening? WHAT I AM DOING library(GenomicFeatures) gff_path <- '/path/to/gff3' makeTxDbFromGFF(file = g ...
genome R annotation written 9 months ago by manuelmendoza40
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Answer: A: Trinity de novo assembly without reference genome (community metatranscriptome)
... You should make only one consensus transcriptome with all your reads. After that, make the differential gene expression, both analyses can be made using Trinity. Overmore, you should use Trinotate for functional annotation. You will need to use a cluster with approx 250G of RAM during 24 hours. Foll ...
written 11 months ago by manuelmendoza40
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Answer: A: Bam to read counts for differential expression analysis
... I use StringTie... Another option is Cufflinks ...
written 12 months ago by manuelmendoza40
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StringTie - A transcript matching to multiple genes
... Hello! I am trying to analyse differential gene expression in 83 samples split up into three groups following the protocol described by Pertea et al., 2016 (doi:10.1038/nprot.2016.095). Now I have two CSV files for each pairwise comparison, one with the transcripts results and other with gene res ...
R alignment rna-seq assembly written 12 months ago by manuelmendoza40
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Comment: C: HISAT2 - "Encountered internal HISAT2 exception (#1)"
... Hello manuelmendoza! We believe that this post does not fit the main topic of this site. Done! For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we'll be hap ...
written 13 months ago by manuelmendoza40
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(Closed) HISAT2 - "Encountered internal HISAT2 exception (#1)"
... Hello everyone! I am a noob in bioinformatics. Now I am trying to run "new Tuxedo" protocol using HISAT. But I have the following problem: Error: Encountered internal HISAT2 exception (#1) Command: /opt/cesga/hisat2/2.0.5/gcc/5.3.0/bin/hisat2-align-s --wrapper basic-0 -p 8 --dat -x GRCh38 ...
software error genome alignment rna-seq written 13 months ago by manuelmendoza40
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Comment: C: Trouble using TopHat (bowtie index genome.*.bt2l)
... Thaks so much! I've just got the publication =D ...
written 13 months ago by manuelmendoza40
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Comment: C: Trouble using TopHat (bowtie index genome.*.bt2l)
... I just have tried it but it does not work: ln -s /path_to/Hsa38/Sequence/Bowtie2Index/genome.* ln: target '/path_to/Hsa38/Sequence/Bowtie2Index/genome.rev.2.bt2' is not a directory ...
written 13 months ago by manuelmendoza40
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Trouble using TopHat (bowtie index genome.*.bt2l)
... Hello! I'm just starting to use tophat and I have a little problem which I am not able to solve. I wanna align several human transcriptomes, so I have downloaded the reference human genome (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/NCBI/GRCh38/Homo_sapiens_NCBI_GRCh38.tar.gz) and n ...
software error alignment rna-seq written 13 months ago by manuelmendoza40 • updated 13 months ago by Kevin Blighe33k

Latest awards to manuelmendoza

Scholar 9 months ago, created an answer that has been accepted. For A: Trinity de novo assembly without reference genome (community metatranscriptome)

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