User: vahapel

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vahapel160
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160
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Location:
Turkey
Last seen:
1 year, 11 months ago
Joined:
4 years, 10 months ago
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Posts by vahapel

<prev • 32 results • page 1 of 4 • next >
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Comment: C: PacBio Quality checking tool
... Hi genomax, Thank you for your answer, I think problem is solved. First, I glance at the sequence length distribution and RQ value (reflecting read quality in fastq header) of service-provided ".fastq" files, noticing that minimum sequence length is set to 35 and quality value ranged from 75 to 80 ...
written 2.4 years ago by vahapel160
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PacBio Quality checking tool
... Hi All, We obtained the “.bax.h5” and “.fastq” files after PacBio sequencing service and I also converted “.bax.h5” to “.fasta” and “.fastq” file types using Pls2fasta tool. However, I could not get the same read numbers in fastq files (between service provided “.fastq” and my-converted “fastq fi ...
assembly next-gen sequencing written 2.4 years ago by vahapel160 • updated 2.3 years ago by Biostar ♦♦ 20
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Comment: C: Script for getting summary statistic of any genome using GTF or GFF3 ?
... Hi Juke-34, thank you for introducing "GAG" to me, it is perfectly suited for the project. ...
written 3.6 years ago by vahapel160
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Comment: C: Script for getting summary statistic of any genome using GTF or GFF3 ?
... Dear h.mon, BedTools is perfect in many aspect, during my search for gff3 parsing, I encountered some very useful tools; gffutils: https://pythonhosted.org/gffutils/contents.html# (I strongly recommend) gff-ex: http://bioinfo.icgeb.res.in/gff/ (very simple and useful) process_exonerate_gff3.pe ...
written 3.6 years ago by vahapel160
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Answer: A: How to figure out coding sequence based on the results of blastx
... If you did your analysis in de novo trascriptome assembly manner, I recommend "TransDecoder Tool"  (https://transdecoder.github.io/), it is good in terms of quality and fastness. ...
written 3.6 years ago by vahapel160
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Script for getting summary statistic of any genome using GTF or GFF3 ?
... Hi All, Nowadays, I am looking for a script for obtaining summary statistics such as; transcript number, base numbers, length, intron length etc., using GTF/GFF3 file(s) and genome ?  Thank you for all your help ! ...
genome gene sequence written 3.6 years ago by vahapel160 • updated 3.6 years ago by Juke-342.2k
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Answer: A: Alternatives to Tophat and Trinity for calculating differentially expressed gene
... Hi, If you determine the differentially expressed transcripts after de novo transcriptome assembly, I recommend to you using "Corset: enabling differential gene expression analysis for de novo assembled transcriptomes". By obtaining the RNA-Seq count data, you can try any of package; DeSeq2, edgeR, ...
written 3.8 years ago by vahapel160
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Answer: A: plant version of biomart
... Plaza v3.0 is very useful especially in terms of comperative genomics and partly functional annotations. http://plaza.psb.ugent.be/ ...
written 3.8 years ago by vahapel160
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Answer: A: Softwares for gene annotation
... You can use Annocript; https://github.com/frankMusacchia/Annocript for functional annotations (BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission). I think that it is one of best free de novo transcriptome annota ...
written 3.9 years ago by vahapel160
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Comment: C: Finding ortholog transcript sequences after de novo transcriptome assembly
... Hi Mark, Thank you for your response and I think that RHB will help me on the topic! New version Inparanoid v8 (http://inparanoid.sbc.su.se/cgi-bin/index.cgi) is also good option. ...
written 4.0 years ago by vahapel160

Latest awards to vahapel

Popular Question 24 months ago, created a question with more than 1,000 views. For Script for extracting data from a tab-delimited file
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Script for extracting data from a tab-delimited file
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Script for extracting data from a tab-delimited file
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Script for getting summary statistic of any genome using GTF or GFF3 ?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Script for extracting data from a tab-delimited file
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Extraction of first sequences from a big fasta file
Scholar 3.8 years ago, created an answer that has been accepted. For A: plant version of biomart
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: plant version of biomart

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