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Forum: Bioinformatics 10-17-2019, 02:49 PM
Replies: 0
Views: 638
Posted By jmartin
is DCJ distance affected by contig number?

I've done some clustering based on the DCJ (Double-Cut-or-Join) distances reported by the Mauve alignment program for 10 assemblies vs. a common reference. I used Mauve to re-order each of my...
Forum: Bioinformatics 08-26-2019, 03:12 PM
Replies: 0
Views: 648
Posted By jmartin
Tool for annotating repeats on mitochondrial genome

Are there specific tools for annotating repeats on a mitochondrial genomes? Or should I be OK just using RepeatModeler / RepeatMasker?

Are there any special issues I need to be aware of when...
Forum: Bioinformatics 05-02-2019, 10:13 AM
Replies: 1
Views: 634
Posted By jmartin
Identification of Internal Transcribed Spacers (ITS) in non-fungal eukaryotes

Is there any software that can identify the ITS regions within a denovo assembly of a nematode species? Or do I pretty much just have to manually annotate the 18s, 5.8s & 28s and pick out regions...
Forum: Bioinformatics 01-30-2019, 11:43 AM
Replies: 0
Views: 606
Posted By jmartin
ncRNA copy number in eukaryotic genomes

I'm annotating tRNAs & rRNA genes in a flatworm species using the tools Infernal, RNAmmer & tRNAscan-SE. My plan was to compare the outputs in the hopes that for future worms I could just run...
Forum: Bioinformatics 11-13-2018, 04:30 PM
Replies: 0
Views: 591
Posted By jmartin
mapping V1V3 region 16s to a database of V1V3+V3V5 region 16s

There is a table of 'most wanted genomes' (MWGs) from the Human Microbiome project that lists the 2698 organisms that the community generally thinks would be useful to have genome sequence. The...
Forum: Pacific Biosciences 10-26-2018, 02:38 PM
Replies: 5
Views: 2,978
Posted By jmartin
I've got PBJelly running now using subreads for...

I've got PBJelly running now using subreads for which I've swapped in q30 values. I'm running one instance w/ all defaults and another using support -x "--capturedOnly" in the hopes to minimize the...
Forum: Pacific Biosciences 10-22-2018, 01:51 PM
Replies: 5
Views: 2,978
Posted By jmartin
I am using subreads that were generated from the...

I am using subreads that were generated from the smrt link using the 'bam to fastx' method and they do appear to all be quality 0. Is there some way to force PBJelly to assume all quality values is...
Forum: Pacific Biosciences 10-17-2018, 02:57 PM
Replies: 5
Views: 2,978
Posted By jmartin
PBJelly novice needs advise

I have a supernova assembly of 10x genomics data for which I also have 4 smrt cells of PacBio Sequel data. The general workflow of my efforts so far have been:

supernova (using 10x genomics data)...
Forum: Bioinformatics 08-31-2018, 05:29 PM
Replies: 0
Views: 824
Posted By jmartin
Need tool to report mapped amino acid frequency per position along reference

I need to generate translated alignments of reads along a reference (which is an amplicon that is 100% coding), and I want to report the frequency of each amino acid at each position along the...
Forum: Bioinformatics 04-19-2018, 01:19 PM
Replies: 3
Views: 638
Posted By jmartin
Thanks for the suggestion, mosdepth is just what...

Thanks for the suggestion, mosdepth is just what I need!

@Mizzou55 it looks like its reporting the average depth across the requested intervals. If you want depths at specific positions in...
Forum: Bioinformatics 04-18-2018, 02:15 PM
Replies: 3
Views: 638
Posted By jmartin
Need simple way to get coverage per 10kb interval on reference

Is there a tool that can tell me coverage per some uniform interval along a set of reference contigs? I know I could use bedtools coverage and build a bed file defining the intervals, but I was...
Forum: Bioinformatics 02-28-2018, 11:13 AM
Replies: 0
Views: 640
Posted By jmartin
denoising data for genera level OTU building

I am planning on running qiime's pick_open_reference_otus.py on a mixed set of 300-400 16s samples, some of which are Illumina MiSeq and some are 454. At this point I have only fasta & fastq data,...
Forum: Bioinformatics 11-28-2017, 11:50 AM
Replies: 2
Views: 747
Posted By jmartin
ncbi blastn database error

I have an assembly that I want to screen against genbank's NT database. I'm using ncbi blastn v2.6.0+ and I first downloaded the pre-indexed NT from:

ftp.ncbi.nlm.nih.gov/blast/db/nt*.tar.gz
...
Forum: Bioinformatics 09-11-2017, 01:12 PM
Replies: 4
Views: 967
Posted By jmartin
I'll try the GATK ValidateSamFile and see what it...

I'll try the GATK ValidateSamFile and see what it says. GATK tools usually do give helpful error messages and I haven't tried that one yet.

Thanks,
John
Forum: Bioinformatics 09-11-2017, 12:03 PM
Replies: 4
Views: 967
Posted By jmartin
I've no experience with C coding, I mainly stick...

I've no experience with C coding, I mainly stick to scripting languages (perl & python). But I'll take a look at the htslib methods and see if I can muddle through.

Thanks,
John
Forum: Bioinformatics 09-08-2017, 10:31 AM
Replies: 4
Views: 967
Posted By jmartin
help recovering data from bam w/ bad header

I have a bam file that I need to work with to reproduce an issue for some troubleshooting. This bam file was left by a student in a collaborator's lab and we pretty much only have this bam file (no...
Forum: Bioinformatics 07-20-2017, 11:22 AM
Replies: 0
Views: 609
Posted By jmartin
Suggestions for metagenomic gene calling

I have a collection of large metagenomic samples from human stool and I want to characters the gene content per sample. What kinds of tools are available, and what are the best practices? Do you...
Forum: Bioinformatics 05-25-2017, 10:55 AM
Replies: 7
Views: 1,750
Posted By jmartin
It looks like the variation between quasispecies...

It looks like the variation between quasispecies is making it difficult for tadpole to accomplish what I need, which is a sort of 'central' consensus amongst all these quasispecies which can serve as...
Forum: Bioinformatics 05-19-2017, 08:40 AM
Replies: 7
Views: 1,750
Posted By jmartin
Thanks Brian, I'll try playing a bit more. I'll...

Thanks Brian, I'll try playing a bit more. I'll try using tadpole's error correction too in case it deals with cases that I haven't already corrected.
Forum: Bioinformatics 05-18-2017, 05:27 PM
Replies: 7
Views: 1,750
Posted By jmartin
Thanks for the reply! I went and tried Tadpole...

Thanks for the reply! I went and tried Tadpole and I'm trying various things to fine tune the assembly. One thing I'm wondering is if there is a way to do a reference guided assembly in Tadpole? ...
Forum: Bioinformatics 05-17-2017, 05:46 PM
Replies: 7
Views: 1,750
Posted By jmartin
Best way to build consensus of short reads spanning viral gene

I have a collection of Illumina HiSeq 2000 reads that should span a specific coding region in a viral genome. The region these reads cover is 2625bp. What I want to do is generate a consensus of...
Forum: Bioinformatics 10-18-2016, 12:42 PM
Replies: 3
Views: 3,317
Posted By jmartin
Hmm, yeah I wouldn't know what exactly someone...

Hmm, yeah I wouldn't know what exactly someone meant by 'illumina coverage' for a metagenomic sample. Unless you already know the community makeup and know the genome sizes. And even then the...
Forum: Bioinformatics 10-18-2016, 12:17 PM
Replies: 3
Views: 3,317
Posted By jmartin
Its usually best if you can ask the person...

Its usually best if you can ask the person providing that value what exactly they mean if you aren't sure since there are a number of legitimate ways people use the word 'coverage'.

My naive...
Forum: Bioinformatics 10-18-2016, 11:56 AM
Replies: 2
Views: 1,778
Posted By jmartin
Having trouble converting genbank format to gff format

I have a fairly large number of sequin annotation files generated by GenBank's automated PGAP pipeline that I want to convert into bed format. I've been able to use the asn2gb program from the ncbi...
Forum: Bioinformatics 09-30-2016, 02:26 PM
Replies: 6
Views: 2,075
Posted By jmartin
Thanks thats very helpful!

Thanks thats very helpful!
Showing results 1 to 25 of 74

 


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