User: juanma_lace

gravatar for juanma_lace
juanma_lace20
Reputation:
20
Status:
New User
Location:
Argentina
Last seen:
4 years, 7 months ago
Joined:
4 years, 11 months ago
Email:
j**********@hotmail.com

Posts by juanma_lace

<prev • 12 results • page 1 of 2 • next >
9
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Which bioinformatics books would you recommend to a programmer / software engineer?
... I'm a graduate Software Engineer and  new in the field of Bioinformatics. Which book would you recommend to me? thank you! ...
software bioinformatics book written 4.7 years ago by juanma_lace20 • updated 4.7 years ago by RamRS24k
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Comment: C: How to programatically run a blast to ensembl and obtain GFF from own FASTA
... I see, thank you for your answer. Upvoted ...
written 4.7 years ago by juanma_lace20
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Comment: C: How to programatically run a blast to ensembl and obtain GFF from own FASTA
... thanks, I've edited the question ...
written 4.7 years ago by juanma_lace20
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How to programatically run a blast to ensembl and obtain GFF from own FASTA
... Hi, I'm using python and I have a wheat genome portion in  .FASTA format (nucleotides). I want to run BLAST against ENSEMBL and obtain genes annotations in .GFF3 programatically in order to use those items in a custom pipeline.   Any ideas? thank you in advance   EDITED: My vision is: 1- Ru ...
gff3 ensembl blast python written 4.7 years ago by juanma_lace20
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Comment: C: Transform smallRNA SRA (Illumina) sequences to FASTA
... thank you for the sarcasm, anyway it does not answer my question. My question is about removing the adaptors, not just converting.  ...
written 4.7 years ago by juanma_lace20
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Comment: C: Transform smallRNA SRA (Illumina) sequences to FASTA
... I see that illumina-dump creates a lot of files, how can I get the fasta from those files ...
written 4.7 years ago by juanma_lace20
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Transform smallRNA SRA (Illumina) sequences to FASTA
... Hi all, I'm running an analysis of small RNA and I want to use some libs from NCBI in SRA (Illumina). The problem is that all the reads are 35 bp long (I understand they have some kind of adaptors). I want to know how to obtain the real fasta sequences programatically (I want to use them in a pip ...
fasta illumina smallrna adaptor sra written 4.7 years ago by juanma_lace20 • updated 4.3 years ago by Biostar ♦♦ 20
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Answer: A: Strange "Error: OID not found" in NCBI's blastdbcmd
... Deleting previous generated databases with makeblastdb solve the issue. I was getting no error, but the database was not being generated again. ...
written 4.8 years ago by juanma_lace20
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Strange "Error: OID not found" in NCBI's blastdbcmd
... I'm getting a OID not found when executin blastdbcmd. My file is as follows: >cat data/4D/4ds_newbler2.6_shotgun_lmp_scaffolds.fasta.splitted | grep scaffold00001_37_1_21 >scaffold00001_37_1_21 And I run >makeblastdb -dbtype 'nucl' -in data/4D/4ds_newbler2.6_shotgun_lmp_scaffolds.fas ...
fasta blastcmd blast makeblastdb blastdbcmd written 4.8 years ago by juanma_lace20 • updated 4.8 years ago by Siva1.6k
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Cannot run UNAfold, error in shared library
... I'm having troubles running UNAFold.  I'm executing a perl script (sumirofold.pl) that calls for a UNAFold query. The UNAFold return an error as next: perl /usr/bin/UNAFold.pl -X 1 --ann ss-count 1_scaffold01901.fsa Checking for boxplot_ng... found, supports Postscript Checking for hybrid-plot-n ...
chip-seq rna-seq unafold written 4.8 years ago by juanma_lace20 • updated 3.0 years ago by Biostar ♦♦ 20

Latest awards to juanma_lace

Popular Question 4.7 years ago, created a question with more than 1,000 views. For How to programatically run a blast to ensembl and obtain GFF from own FASTA
Scholar 4.8 years ago, created an answer that has been accepted. For A: Strange "Error: OID not found" in NCBI's blastdbcmd

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