User: reza

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reza160
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160
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Location:
Iran
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4 days, 9 hours ago
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1 year, 4 months ago
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i am here to learn

Posts by reza

<prev • 76 results • page 1 of 8 • next >
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Comment: C: receive GC-content profile for a given window-size and splitting multi fasta fil
... it does not work for me. cat DROM_5000.fa | ./pythonscript.py File "./pythonscript.py", line 9 name = # process your line accordingly to get the sequence / scaffold name ^ SyntaxError: invalid syntax ...
written 4 days ago by reza160
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Comment: C: receive GC-content profile for a given window-size and splitting multi fasta fil
... the following format is for GC-content profile for a given window-size (50000) that freec-control need it. first column:chromosome name; column two: window-size, column tree: GC-content, column four: percentage of ACGT-letter per window (1-poly(N)%). the file containing the following information is ...
written 4 days ago by reza160 • updated 4 days ago by genomax39k
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receive GC-content profile for a given window-size and splitting multi fasta file into separate fasta files by contigs name for running control-free
... i have two question about control-FREE 1.how can i receive GC-content profile for a given window-size (50000) for a reference genome in fasta file? 2.how can i split multi fasta file into separate fasta files by contigs name? (original fasta have ~32000 contig and after separation i must have 3200 ...
splitting fasta written 4 days ago by reza160 • updated 4 days ago by genomax39k
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how to create target region track for CNV detection using Biomedical genomics workbench
... i want to identify CNV using WGS data. i mapped my reads into reference genome and now using Biomedical genomics workbench, i wanna detect CNV in whole genome not targeted region but copy number variation tool in Biomedical genomics workbench require target region track. i read software manual but I ...
target region clc cnv written 13 days ago by reza160
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change fastq header
... i have a fastq file that have headers like "@HWI-ST916:209:XXXX:2:1101:1104:1915 1:N:0:", Now i want to convert them like "@HWI-ST916:209:XXXX:2:1101:1104:1915/1" how can i do it? thanks in advance ...
fastq written 28 days ago by reza160 • updated 28 days ago by Pierre Lindenbaum102k
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Comment: C: how to download all bacterial complete genome from RefSeq?
... thank you genomax, it worked for me very well ...
written 6 weeks ago by reza160
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how to download all bacterial complete genome from RefSeq?
... hi i want to download all Bactria complete genome from Refseq in fasta format? I googled and find below link: https://www.biostars.org/p/61081/#180944 but this way cause to download *cds_from_genomic_fna.gz and *rna_from_genomic_fna.gz too. i want only *genomic_fna.gz for my work. how can i do it ...
genome bactria sequence written 7 weeks ago by reza160 • updated 7 weeks ago by Ram12k
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Comment: C: Extract all paired reads from sam file
... do you want to extract paired end reads that map to reference in to fastq files? ...
written 11 weeks ago by reza160
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Comment: C: Workflow for annotating repeat elements
... i used following workflow to annotation of repetitive elements in my own work one new genome: ./BuildModeler -name your_desired_name input_genome.fa ./RepeatModeler -engine ncbi -pa 15 -database your_desired_name ./RepeatMasker -pa 16 -gff -xsmall -lib /path/to/conseni.fa.clas ...
written 3 months ago by reza160 • updated 3 months ago by WouterDeCoster24k
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Comment: C: Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
... i used bioawk to calculate mean quality score of fastq and it gave me one mean per each read. now, how can i calculate overall quality mean using output of bioawk? ...
written 4 months ago by reza160

Latest awards to reza

Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Problems with Trimmomatic PE output files

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