User: Manuel Mendoza

Reputation:
10
Status:
New User
Location:
University of Vigo, Spain
Last seen:
10 minutes ago
Joined:
3 years, 6 months ago
Email:
m*********************@gmail.com

I am MSc student at University of Vigo (CINBIO) with background in marine biology. I work on NGS-data, specially RNA-Seq.

Actually I am working with different species of genus Elysia transcriptome and Mytilus genome at Evolutionary Genomics Group.

Posts by Manuel Mendoza

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Which pipeline is the best for differentinal gene expression analysis (edgeR, DE
... It may be easier use salmon + edgeR afeter the assembly and annotation (Trinity-Trinotate) ...
written 3 days ago by Manuel Mendoza10
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Comment: C: Which pipeline is the best for differentinal gene expression analysis (edgeR, DE
... Trinity is a transcriptome de novo assembler... Do you really need that if you have got a genome of reference? ...
written 4 days ago by Manuel Mendoza10
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PacBio long-reads impact in transcriptome de novo assembly
... Hi! We are strongly interested in assembly a good transcriptome of reference for a non-model organism and build a local database. We have sequenced the same individual with Illumina (150 millions of pair-end reads) and PacBios IsoSeq v3 (2 SMRT cells, one for shorter transcripts, shorter than 5kb a ...
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Answer: A: Which pipeline is the best for differentinal gene expression analysis (edgeR, DE
... It'll strongly depend on your data. If you have a good genome of reference (e.g. human) and you are interested in to study differential transcript usage and discover new potential isoforms, the best idea is Hisat2-StringTie-Ballgown. If you are only interested in study differential gene expression a ...
written 4 days ago by Manuel Mendoza10
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Join multiple SeqRecord with subfeatures in BioPython
... Hi folks, I've created a function that generates a gene sequence and now I wanna concatenate `n` genes together. I've tried reiterative adding using a `for loop` but at the ned, al subfeatures of genes `n > 1`were lost... >>> gene_a = sim_gene(n_exons = 3) >>> gene_ ...
software error python biopytho written 6 months ago by Manuel Mendoza10
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Comment: C: Reads q-index nucleotides one per one
... No, I want the value of q-index per base position for each read... Something like that: Position 01 02 03 04 05 06 ... Read_1 30 31 32 32 30 ... Read_2 30 32 35 34 32 ... ...
written 3.5 years ago by Manuel Mendoza10 • updated 3.5 years ago by WouterDeCoster44k
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Reads q-index nucleotides one per one
... Hello, I am working with fastq file from cDNA. A complete transcriptome was sequenced using Illumina Tech. I want to know the q-index for each read (nucleotide per nucleotide), now I am using ShortRead package (I work with R). Does anyone know how to do it? ...
R rna-seq written 3.5 years ago by Manuel Mendoza10 • updated 3.5 years ago by h.mon31k
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Comment: C: R reads q-score
... Thanks you! I'm going to try it ...
written 3.6 years ago by Manuel Mendoza10
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Comment: C: R reads q-score
... because i want to assemble the proteome after clean up my data ...
written 3.6 years ago by Manuel Mendoza10
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R reads q-score
... Hello, I want to calculate the read q-score (one per one) in a fastq file. Does anyone know any R package to do it? I am working with RNA-seq data and I want to trim the read data (Read q-score>30). How can i do that using R? I don't want to use python. Thanks you. ...
rna-seq written 3.6 years ago by Manuel Mendoza10 • updated 2.4 years ago by Biostar ♦♦ 20

Latest awards to Manuel Mendoza

Popular Question 2.4 years ago, created a question with more than 1,000 views. For R reads q-score
Autobiographer 3.6 years ago, has more than 80 characters in the information field of the user's profile.

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