User: Leonardo

gravatar for Leonardo
Leonardo30
Reputation:
30
Status:
New User
Location:
Brazil
Last seen:
1 year, 3 months ago
Joined:
6 years, 2 months ago
Email:
l*****@hotmail.com

Posts by Leonardo

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Qiime - problem with biom package in normalization
... I've just got into this issue while installing Tax4Fun and that's how I fixed (R 3.5.3): Went to the development page on GitHub: https://github.com/joey711/biom Then "made available through Cran" and there "archive". Downloaded the latest version (biom 0.3.12.tar.gz) Installing: install.packa ...
written 15 months ago by Leonardo30
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Comment: A: MiSeq or HiSeq for metatranscriptome sequencing
... Hi, any updates on that? I am having the same question here ...
written 2.1 years ago by Leonardo30
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Comment: C: How Does One Decide Which Bacterial Taxonomic Classification To Use: Rdp, Silva
... HI crespialba, Would you mind to clarify where that taxmap_embl file is? I couldn't find it in both Silva and NCBI databaases. ...
written 2.1 years ago by Leonardo30
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Answer: A: Blastdbcheck Error
... Years after but error still persists. In the following link you can find a solution provided by user "carlosproca", which just worked for me. It is something related to taxon id files. http://seqanswers.com/forums/archive/index.php/t-34826.html ...
written 2.7 years ago by Leonardo30
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Comment: C: Download All The Bacterial Genomes From Ncbi
... For those from the future: have a look at "cseto" complement down there regarding updates in the .fna links and avoid spending hours of your precious time trying to fix it (like me =)). The above sed command is now out of date because NCBI changed link adresses. ...
written 2.7 years ago by Leonardo30
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Comment: C: Download All The Bacterial Genomes From Ncbi
... Oh my!!! So many thanks! Spent hours trying to figure it out. ...
written 2.7 years ago by Leonardo30
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Comment: C: Create GFF from de novo assembly to input on htseq-counts
... Well, the counts differences between bowtie.bam and RSEM.bam were hudge. Greater than I have thought. As an example:  geneID    C_bt2  T_bt2  C_rsem T_rsem transcript_27 324 1925 164 901 transcript_28 2 29 0 1 transcript_29 0 0 0 0 transcript_30 0 0 0 0 transcript_35 6 24 0 0 transcript_36 582 387 ...
written 6.2 years ago by Leonardo30
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Comment: C: Create GFF from de novo assembly to input on htseq-counts
... Hi Devon, another doubt: should this counting non-multimappers step be done by using a outputed RSEM.bam or a BOWTIE2.bam? I'm asking it because mapping with bowtie2 in local mode can produce more alignments than using RSEM, because of RSEM don't consider as valid gapped alignments. ...
written 6.2 years ago by Leonardo30
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Comment: C: Create GFF from de novo assembly to input on htseq-counts
... The assembly wasn't constructed with my data, but with data from the same species in different conditions. I'm using this assembly to map my 14 samples. ...
written 6.2 years ago by Leonardo30
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Comment: C: Create GFF from de novo assembly to input on htseq-counts
... Thanks Devon, I'll try it! ...
written 6.2 years ago by Leonardo30

Latest awards to Leonardo

Great Question 2.1 years ago, created a question with more than 5,000 views. For Create GFF from de novo assembly to input on htseq-counts
Popular Question 6.2 years ago, created a question with more than 1,000 views. For Create GFF from de novo assembly to input on htseq-counts

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