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Forum: Genomic Resequencing 08-20-2018, 11:05 AM
Replies: 2
Views: 3,399
Posted By htetre
I am currently trying to call SNPs with the...

I am currently trying to call SNPs with the problematic file alone. I am able to get expected results, ie high support for one GT and low support for the other two GT with the "non-problematic" file.
Forum: Genomic Resequencing 08-15-2018, 10:01 AM
Replies: 2
Views: 3,399
Posted By htetre
PL high support for each GT for all SNPS

Hello,

I have two populations I am trying to discover SNPs for. In my .vcf file one population has the GT and the PL is 0,0,0 for every single snp ie 0/1, 0/0, and 1/1. Does anyone know where I...
Forum: Bioinformatics 07-26-2017, 02:17 PM
Replies: 7
Views: 1,942
Posted By htetre
Hello, I have found my problem, and it...

Hello,

I have found my problem, and it resides in the gff file I have been using. It only contained the gene not gene_exon information. Once I used the correct gff file the genome database was...
Forum: Bioinformatics 07-07-2017, 05:13 AM
Replies: 7
Views: 1,942
Posted By htetre
Well, up to now my vcf file is based on the most...

Well, up to now my vcf file is based on the most recent Sorghum genome assembly and that assembly is not part of snpeff. But with the difficulty I am having to build genome database I'm thinking of...
Forum: Bioinformatics 07-06-2017, 11:26 AM
Replies: 7
Views: 1,942
Posted By htetre
Thank you fin swimmer, I have changed that...

Thank you fin swimmer,

I have changed that now, thanks to you. Now it is definitely going to the correct path. However I have determined that my database was never built correctly in that I do not...
Forum: Bioinformatics 07-05-2017, 08:05 AM
Replies: 7
Views: 1,942
Posted By htetre
fin swimmer, Thank you for your reply. ...

fin swimmer,

Thank you for your reply.

This is what I have in my config file:

#Sorghum bicolor genome, version 3.0.1
Sorghum.genome : Sorghum

And this is the error I am getting when...
Forum: Bioinformatics 07-03-2017, 12:27 PM
Replies: 7
Views: 1,942
Posted By htetre
snpEff eff with built genome database

Hello,

I am having trouble annotating my vcf file using a database that I built. It seems as though snpEff wants to go to sourceforge.net to retieve a built database. Can someone help me identify...
Forum: Bioinformatics 07-02-2017, 10:59 AM
Replies: 3
Views: 1,144
Posted By htetre
Hello, Did you ever find a good tool to...

Hello,

Did you ever find a good tool to filter out SNPs with genotypes across your samples?

I am looking to do the same, filter sites that are invariant across samples that are in a single vcf...
Forum: Bioinformatics 06-22-2017, 11:58 AM
Replies: 8
Views: 9,113
Posted By htetre
Keep all chromosomes and remove scaffolds

Hello,

I am trying to do something similar, I want to keep information for 10 chromosomes (Chr01-10) and remove the scaffold SNP information in my vcf file.

This is the code I have run...
Forum: Genomic Resequencing 06-20-2017, 01:56 PM
Replies: 1
Views: 3,974
Posted By htetre
issue resolved

Issue was resolved for this problem. Turns out the bcftools version 1.3 uses -call instead of the older version that uses -view. And the reason it crashed after chr01 was because I did not allot...
Forum: Genomic Resequencing 06-18-2017, 10:08 AM
Replies: 1
Views: 3,974
Posted By htetre
mpileup only calling snps for chr1 not entire genome

Hello,

I am having a problem when trying to call SNPS from two alignment files, and this also happened when I tried calling SNPs from only 1 alignment file. My problem is I am only getting SNPs...
Forum: Bioinformatics 03-02-2017, 10:57 AM
Replies: 8
Views: 2,883
Posted By htetre
Thank you so much for the information! I will...

Thank you so much for the information! I will give this a try.

Thank you again
Forum: Bioinformatics 02-28-2017, 07:31 AM
Replies: 8
Views: 2,883
Posted By htetre
Thanks, I am working with Sorghum bicolor...

Thanks,

I am working with Sorghum bicolor which there is an available kegg db for, however it is based on the v1 genome ID and we are currently at v3 with different gene_IDs. My work has been...
Forum: Bioinformatics 02-25-2017, 12:37 PM
Replies: 8
Views: 2,883
Posted By htetre
KEGG set from annotation file

Hello,

Can you direct me to information on how you constructed your gmt file for GAGE analysis? I have an annotation file (.txt) that contains my geneID, KEGG, KO, KOG, and GO information.

I...
Forum: RNA Sequencing 02-09-2017, 01:55 PM
Replies: 0
Views: 1,046
Posted By htetre
GOSeq annotation file: hierarchical GO terms

Hello,

I have an annotation file from Phytozome that has the parent child structure, (i.e. GO:0016459,GO:0005524,GO:0003774,GO:0005515). When I use this in GOSeq R analysis GO terms with the...
Forum: Bioinformatics 10-30-2016, 11:49 AM
Replies: 2
Views: 3,488
Posted By htetre
HISAT2 _spliced_sites with a gff3 file

Hello,

I am trying to extract_splice_sites using the python script provided by HISAT2 to use in the downstream alignment in HISAT2. However the reference genome that I am using, the most recent...
Forum: Bioinformatics 10-30-2016, 09:24 AM
Replies: 155
Views: 66,209
Posted By htetre
Hello, I am trying to use featureCount with...

Hello,

I am trying to use featureCount with a bam file that aligned using Hisat2 with an indexed genome and spliced sites file created from a gtf file. Now I am using the same gtf file in...
Forum: Bioinformatics 04-29-2014, 06:53 AM
Replies: 9
Views: 9,450
Posted By htetre
Thanks dpryan for the sort code. It works great...

Thanks dpryan for the sort code. It works great for me except that in my sorted file it has the sequence name twice. ie >106x2447112 >106x2447112.

What part of the code removes the printing the...
Forum: Bioinformatics 03-03-2014, 01:02 PM
Replies: 4
Views: 9,164
Posted By htetre
Thank you for your explanation, it is very...

Thank you for your explanation, it is very helpful. I am using BWA for mapping, in testing parameters I tend to get a plateau of reads aligned. I was wondering why this is? Is it due to mapping...
Forum: Bioinformatics 11-11-2013, 11:44 AM
Replies: 7
Views: 2,256
Posted By htetre
Hello, I am using genometools and yesterday...

Hello,
I am using genometools and yesterday when using suffixerator I was provided an error message of illegal characters. When I opened my fasta file in Textwrangler and checked for the invisibles...
Forum: Bioinformatics 10-21-2013, 09:54 AM
Replies: 8
Views: 5,424
Posted By htetre
Hello, I am trying to translate my DNA...

Hello,

I am trying to translate my DNA sequences to protein with fasta files that can contain as many as 7,000 sequences. Instead of translating to all 6 reading frames I would like to perform a...
Forum: Bioinformatics 08-23-2013, 08:05 AM
Replies: 99
Views: 40,927
Posted By htetre
Unable to download MapView

Hello,

I have ace files that I would like to view and came across your MapView Software as a solution. However, I am unable to get any of the links in above messages to download a the program?
...
Forum: Bioinformatics 08-14-2013, 01:36 PM
Replies: 30
Views: 10,405
Posted By htetre
Hello Marina_P, I just started using...

Hello Marina_P,

I just started using RepeatExplorer, as well. Yes and there are many graphs. I actually came on the forum to see if there is any discussion about the program to help me understand...
Forum: Bioinformatics 07-26-2013, 01:29 PM
Replies: 24
Views: 7,728
Posted By htetre
Get the hang of how to make the adapter sequence...

Get the hang of how to make the adapter sequence file? I wonder if I did that wrong. Do you just make a fasta file with your adapters, ie barcode sequence with a header? Or is there something I...
Forum: Bioinformatics 07-26-2013, 01:05 PM
Replies: 24
Views: 7,728
Posted By htetre
Hello I have a python script to sync my paired...

Hello I have a python script to sync my paired end reads after quality filtering and am running into errors since I have Python 3 on my computer. Would someone mind looking at the problem area...
Showing results 1 to 25 of 28

 


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