User: Bioinfo

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Bioinfo20
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Morocco
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Posts by Bioinfo

<prev • 99 results • page 1 of 10 • next >
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Comment: C: Count number of Genes in GFF3 file (Prokka output)
... Thank you for your answer but i think that gene is repeated more than one time for one gene , is like that scaffold1_size61041 prokka gene 29 829 . + . ID=wAse_00001_gene;locus_tag=wAse_00001 scaffold1_size61041 Prodigal:002006 CDS 29 829 . + 0 ID=wAse_00001;Parent=wAse_00001_gene;inferenc ...
written 9 days ago by Bioinfo20
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Count number of Genes in GFF3 file (Prokka output)
... Hello . please i have run prokka on eight strains and i have eight GFF files , i want to count number of genes in each GFF file , please tell me how to do that Thank you ...
gene assembly sequence sequencing written 9 days ago by Bioinfo20 • updated 9 days ago by Juke344.8k
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Core genome analysis for viruses
... Hello everyone! I've been trying to build core genomes of HIV and SIV viruses using Roary. But I keep getting 0 core genes. I've tried changing "minimum percentage identity for blastp" parameter. I used the default value first and here's the result : Core genes (99% <= strains <= 100%) 0 ...
gene assembly sequence sequencing written 15 days ago by Bioinfo20
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Comment: C: what is the parametrs i should take in consideration to choose the best assembly
... Thank you very much for your answer , and very sorry for late reply i used shovill for assembly ( it contains spades inside ) ahh also i have to mention that i used spades with specefic kmer ( the one gived by Unicycler ) so for each sequencing technic i have two assembly file : Default and kmerX( ...
written 5 months ago by Bioinfo20
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Comment: C: what is the parametrs i should take in consideration to choose the best assembly
... Hello Thank you for your reply , what do you mean by taking both miSeq and HiSeq is taking the mixed contigs file or taking the fileafter removing duplication ? ...
written 5 months ago by Bioinfo20
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what is the parametrs i should take in consideration to choose the best assembly
... Hello Biostar ! Please i have question i did sequencing of five strains with two datasets (Hiseq Data and Miseq Data ) so for each strain i have Hiseq contigs file and Miseq contigs file (and mixed Hiseq Miseq contigs file) for exemple let s say i have strain A , so i have Hiseq_A_R1.fastq Hiseq_ ...
assembly sequence alignment sequencing written 5 months ago by Bioinfo20 • updated 5 months ago by Michael Dondrup47k
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Comment: C: How to remove duplicated sequences without using any software
... Hello , thank you very much for your reply and your suggestions , and sorry for late reply Yes my principal aim was to improve assembly results for that i merged results of assembly (the contigs files ( because i had Hiseq data and Miseq Data) after that i removed duplicated sequences using cd-h ...
written 5 months ago by Bioinfo20
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Comment: C: How to remove duplicated sequences without using any software
... Ahh yes it works now , thank you :D ...
written 5 months ago by Bioinfo20
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Comment: C: How to remove duplicated sequences without using any software
... yes i already used it but it didn't work 0 duplicated records removed and i still get the same error msg in prokka ...
written 5 months ago by Bioinfo20
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How to determine the number of number of nucleotides
... Hello Biostar i hope you're doing well please how can i determine number of contigs that are higher than a size , ( i want to determine how many contigs that are higher than N50 ) Thank you ...
sequence assembly alignment sequencing written 5 months ago by Bioinfo20 • updated 5 months ago by Kevin Blighe66k

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