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Forum: Bioinformatics 10-31-2019, 10:36 AM
Replies: 0
Views: 402
Posted By JWolters
Understanding Sequence Ontology Relationships in GFF3

I am working on a pipeline to go from annotations from a tool through several steps ultimately to a gff file in GFF3 format. The last step is conversion from a genbank flatfile to gff3.

For the...
Forum: Bioinformatics 12-06-2016, 01:59 PM
Replies: 3
Views: 1,523
Posted By JWolters
I haven't applied any adapter or quality trimming...

I haven't applied any adapter or quality trimming post-alignment, but it is possible that I have removed low quality mates.

I will try filtering discordant mappings immediately post alignment...
Forum: Bioinformatics 12-06-2016, 01:22 PM
Replies: 3
Views: 1,523
Posted By JWolters
Foolproof ways to remove discordant read pairs

I am tearing my hair out trying to run an application that requires all reads be properly mapped 1 time in the correct orientation.

I have applied various GATK filters to the data during indel...
Forum: Bioinformatics 09-20-2016, 07:55 AM
Replies: 0
Views: 839
Posted By JWolters
Tools for Detecting Recombination in Closely Related Sequences

Hi all,

I am working with some fungal mtDNAs and am hoping to detect evidence of recombination.

My main issue is that these sequences (~100) are all within a species and the coding sequences...
Forum: Bioinformatics 09-02-2016, 08:22 AM
Replies: 5
Views: 1,694
Posted By JWolters
Apologies for a lack of clarity on my part, I...

Apologies for a lack of clarity on my part, I have limited experience with short-read alignment. Thank you for your super fast replies.



The "parental" genomes are yeast mitochondrial genomes...
Forum: Bioinformatics 09-01-2016, 01:44 PM
Replies: 5
Views: 1,694
Posted By JWolters
Hate to double post but I thought this might be...

Hate to double post but I thought this might be better posted in this context rather than in the main BBmap support thread.

When I align my sequencing reads from the pool to the mixed reference, I...
Forum: Bioinformatics 08-24-2016, 12:24 PM
Replies: 5
Views: 1,694
Posted By JWolters
Thanks for the tip! I will give it a shot as...

Thanks for the tip!

I will give it a shot as that would be much simpler than having to map separately to each genome, undergo the analysis, and then synthesize the results.
Forum: Bioinformatics 08-19-2016, 07:51 AM
Replies: 5
Views: 1,694
Posted By JWolters
Are gaps in split alignments reported in mpileup output?

Will a split alignment covering a large indel report the intervening bases as gaps, or '-' alleles, in an mpileup output from that alignment?

I have two pooled sequencing samples that represent a...
Forum: Bioinformatics 05-31-2016, 02:16 PM
Replies: 0
Views: 874
Posted By JWolters
Building vcf of known variants for GATK Haplotype Caller with GENOTYPE_GIVEN_ALLELES

I have reads from a pool of recombinants between two parental genomes.

As such, I am only interested in calling variants for the known set of variable alleles between the two parental genomes.
...
Forum: Bioinformatics 10-09-2013, 01:10 PM
Replies: 2
Views: 1,934
Posted By JWolters
Mira: Contigs failing to collapse despite similarity

I have been using MIRA to assemble PacBio data for a very small circular genome and I have been observing a strange result in the output. For several datasets when the contigs are compared to the...
Forum: Bioinformatics 01-17-2013, 11:51 AM
Replies: 2
Views: 1,233
Posted By JWolters
After looking into this, Mauve really might be...

After looking into this, Mauve really might be just the right tool for the job since it can apparently export sets of positionally orthologous features (genes, CDS, tRNA, and so on), thus getting me...
Forum: Bioinformatics 01-17-2013, 08:56 AM
Replies: 2
Views: 1,233
Posted By JWolters
Fasta formatting issues

I am trying to align a multifasta containing various regions of interest from a reference genome and align them to a contig assembled from pacbio reads generated from a related strain, just to get a...
Forum: Bioinformatics 01-15-2013, 02:15 PM
Replies: 2
Views: 2,436
Posted By JWolters
Problems transferring annotations with RATT

Im fairly new to bioinformatics, and I've been having significant trouble using RATT as part of the PAGIT set of tools, and was hoping to find some help here, as I could not find any links to support...
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