User: Mehmet

gravatar for Mehmet
Mehmet170
Reputation:
170
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Trusted
Location:
Japan
Last seen:
5 hours ago
Joined:
2 years, 8 months ago
Email:
m*********@duzce.edu.tr

Posts by Mehmet

<prev • 166 results • page 1 of 17 • next >
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Assembly comparisons and reordering scaffolds
... Dear all, I would like to know your thoughts about comperative genomics. I have two assemblies (reference and draft) of the same species, a worm species. I wanted to compare scaffolds orders in the assemblies. I first used Mauve for alignment and later "move contig order" of Mauve program. Mauve r ...
genome assembly sequence alignment written 2 days ago by Mehmet170
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Comment: C: extract sequences based on ids file
... Thank you very much. It was what I really wanted. ...
written 2 days ago by Mehmet170
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extract sequences based on ids file
... Dear all, I have a ids list that has random order of ids and a fasta file that has the ids. I want to extract sequence of each id from the fasta file. I tried but each time output has different order rather than the order in the ids file. How to extract sequences based on the order in the ids fi ...
gene genome sequence written 2 days ago by Mehmet170 • updated 2 days ago by Alex Reynolds20k
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reorder sequences in fasta file based on ids from different file
... Dear all, I searched for solution but I could not find any. My question is how to reorder sequences in fasta file based on ids from different file. For instance, I have a fasta file, but I want to reorder sequences based on new order of sequences. in fasta file >1 >2 >3 >4 and in id ...
gene genome sequence written 2 days ago by Mehmet170 • updated 2 days ago by h.mon8.7k
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Comment: C: Sorting The Scaffolds After Assembling
... Hi, I would like to ask you, how to replace scaffolds of the draft assembly based on matches with the reference assembly? I used MCM, and I checked that MCMC did not replace scaffolds of the draft assembly based on matches. For instance, scaffold 1 of reference assembly matched with scaffolds 116, ...
written 3 days ago by Mehmet170
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Comment: C: Sorted scaffolds of a draft genome according to a reference genome
... Yes, I did. As I mentioned in my question; "For instance, in first analysis (alignment of the genomes) scaffold 1 of the reference genome matched with scaffold 116 of the draft. When I reordered, the scaffold 116 did not replaced as the first scaffold of the reference genome". What I want is to ...
written 3 days ago by Mehmet170
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Sorted scaffolds of a draft genome according to a reference genome
... Dear all, I would like to sorted scaffolds of a draft genome according to a reference genome. I used Mauve program. It reordered, but when I checked order of scaffolds of the draft genome, it seems that Mauve did not reorder scaffolds of the draft genome. For instance, in first analysis (alignme ...
genome assembly sequence alignment written 3 days ago by Mehmet170
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how to show geographical relationship of contigs from the two assemblies
... Dear All, I want to compare some contigs from two different assemblies of the same animal species. For instance, I want to compare a big contig from assembly A. The big contig will contain small contigs from assembly B. I also want to show haplotype collapse between the assembly A and assembly B. ...
gene assembly alignment sequencing written 12 days ago by Mehmet170 • updated 12 days ago by h.mon8.7k
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a script to be used with qsub command
... Dear all, I need a script to be used with qsub command. Does anyone have a script? I want to submit jobs to a supercomputer, and I need a script for this. ...
assembly next-gen alignment written 20 days ago by Mehmet170 • updated 20 days ago by genomax33k
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Comment: C: What Analysis after Denovo Assembly of RNA-seq of a species?
... Have you tried to use Blast2GO for GO, KEGG and KOG and gene set enrichment analysis? More generally, Blast2GO does functional annotation of a genome or transcriptome data set. ...
written 11 weeks ago by Mehmet170

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