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Search: Posts Made By: gauravdube
Forum: Bioinformatics 07-19-2017, 02:09 AM
Replies: 2
Views: 1,879
Posted By gauravdube
Hi GenoMax, After posting, I have used the...

Hi GenoMax,

After posting, I have used the same command on another assembly which has better genome statistics than the previous one and it worked !!! It seems the problem is with 'probuild', as...
Forum: Bioinformatics 07-17-2017, 03:05 AM
Replies: 2
Views: 1,879
Posted By gauravdube
GeneMark-ES exits with "error, file not found: info/training.fna"

Dear All,
I am trying to use GeneMark-ES Suite 4.32 to predict genes from a fungal genome. But GeneMark exits with:



To run the program, I am using the following command:

./gmes_petap.pl...
Forum: Bioinformatics 10-03-2015, 10:16 AM
Replies: 11
Views: 7,143
Posted By gauravdube
Hi Gabriel, Thank you so much. It worked for...

Hi Gabriel,

Thank you so much. It worked for me.
Forum: Bioinformatics 10-03-2015, 10:11 AM
Replies: 1
Views: 1,197
Posted By gauravdube
Non-ATGC characters, small-case characters and lots of 'N's in fastq file's sequence

Hi All,

My fastq file consists of lot non-ATGC characters. What are these characters and how to handle these?

Commands used:
bwa index ref.fa
bwa aln -t 9 ref.fa D2_R2.fastq -f D2_R2.sai &&...
Forum: Genomic Resequencing 10-03-2015, 10:04 AM
Replies: 5
Views: 19,077
Posted By gauravdube
Hi av_d, My fastq file consists of lot...

Hi av_d,

My fastq file consists of lot non-ATGC characters (you are too are getting in your file, you see that 'W' in your fastq ?). What are these characters and how to handle these?

Commands...
Forum: Bioinformatics 09-16-2015, 01:56 AM
Replies: 1
Views: 2,400
Posted By gauravdube
How to generate a scale for a phylogenetic tree?

Dear All,

I have generated phylogenetic trees for a gene dataset by Neighbor joining and Maximum likelihood methods with 1000 boostrap replicates using PHYLIP v3.69 package. I observed in various...
Forum: Bioinformatics 04-07-2015, 06:35 AM
Replies: 11
Views: 7,143
Posted By gauravdube
Hi gab0, I am facing exactly the same issue...

Hi gab0,

I am facing exactly the same issue of k-mer content. Hence didn't created a different thread when i encountered yours. My question to you is: what is the tool you used to retain the valid...
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