User: Bioblazer

gravatar for Bioblazer
Bioblazer40
Reputation:
40
Status:
New User
Location:
Pune
Last seen:
4 months, 1 week ago
Joined:
2 years, 11 months ago
Email:
m***************@gmail.com

Posts by Bioblazer

<prev • 45 results • page 1 of 5 • next >
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pindel output error
... i have been running pindel like so: ./pindel -f h3rv.fasta -i bam_config.txt -c ALL --Ploidy ploidy_input.txt -o Result_pindel.out -- this is part of bam_config.txt /biobank/seq/muthuk/Mycobacterium_bovis/R100/bamfiles/sorted_bam/SRR5216939_mapped.sort.bam 241.4 SRR5216939 /bio ...
genome alignment next-gen written 5 months ago by Bioblazer40 • updated 3 months ago by Biostar ♦♦ 20
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PASA pipeline running error
... For annotation, I am using PASA pipeline while I am running the following error occurred . Please suggest what is this error ? and how to solve it. ./Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g ATCC.fasta -t transcript.fasta --ALIGNERS blat,gmap I followed all the steps given ...
assembly sequence written 15 months ago by Bioblazer40
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Comment: C: Extract genes from gene list
... Thank you I will try with E-utilities and Batch entrez again ...
written 16 months ago by Bioblazer40
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Comment: C: Extract genes from gene list
... Thank you for reply, If I am not wrong in ensembl whole genome download is possible but those sequence are available in scaffold level. But I need total gene sequence of an organism. ...
written 16 months ago by Bioblazer40
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Comment: C: Extract genes from gene list
... I tried but it did not work. ...
written 17 months ago by Bioblazer40
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Extract genes from gene list
... I have list of genes from *Aspergillus flavus* fungi. From uniprot and Ensembl where I can able to retrieve the protein and CDS sequence respectively for my list of genes in multi-fasta format.But for gene sequence for each time I able to retrieve only one gene at a time. So is there any database ...
sequence sequencing written 17 months ago by Bioblazer40 • updated 17 months ago by genomax47k
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PASA pipeline running error
... For eukaryotic genome annotation , I used PASA pipeline for annotation while running I got the following error How to solve this mysql connection error. root@abc1-desktop:/home/abc1/Desktop/PASApipeline-2.0.2/sample_data# perl Launch_PASA_pipeline.pl -c alignAssembly.config -R -g genome_sampl ...
genome written 17 months ago by Bioblazer40
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Comment: C: RNA seq data analysis
... Follow Tophat+cufflinks protocol (Tuxedo suite) : : http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html otherwise if u dont have replicates with you then follow NOISeq Protocol. ...
written 19 months ago by Bioblazer40
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BRAKER Annotation
... perl braker.pl --genome=ATCC26.fa --bam=accepted_hits.bam use --AUGUSTUS_CONFIG_PATH=/home/abc1/Documents/augustus-3.1/config --GENEMARK_PATH=/home/abc1/Documents/gm_et_linux_64/gmes_petap/gmes_petap.pl --BAMTOOLS_PATH=/home/abc1/Desktop/augustus-3.2.2/bamtools/bin I have used braker for annot ...
annotation written 19 months ago by Bioblazer40
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Comment: C: Mauve installation fails in Windows 8
... Thank you for your kind reply. I forgot to setup environmental variable last time.I should not asked this(these kind of) silly question on these forum.Sorry. I won't do next time. I will try to ask really meaningful question. ...
written 21 months ago by Bioblazer40

Latest awards to Bioblazer

Popular Question 6 months ago, created a question with more than 1,000 views. For DESeq without replicate nbinomTest method
Popular Question 12 months ago, created a question with more than 1,000 views. For BAM header file error

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