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Search: Posts Made By: Protaeus
Forum: Bioinformatics 07-05-2011, 01:59 PM
Replies: 2
Views: 2,353
Posted By Protaeus
BWA: Is alignment summary available?

Is there a tool associated with BWA that can provide a concise overall summary of the alignments/pairing, such as:
1. How many reads did not map?
2. How many single ends mapped?
3. How many reads...
Forum: Bioinformatics 06-06-2011, 04:13 PM
Replies: 1
Views: 1,901
Posted By Protaeus
Obtaining strand calls from BAM/SAM

I am interested in extracting strand info at any or all given positions from an alignment. The purpose is to get info about strand bias in a haploid organism. I know GATK provides strand bias in...
Forum: Bioinformatics 05-24-2011, 04:04 PM
Replies: 1
Views: 1,441
Posted By Protaeus
BWA with reference containing N's

Should I expect anything out of the ordinary by using a reference containing N's when aligning a paired end sample with BWA? It runs fine, which I would expect, but I wasn't sure if there were issues...
Forum: Bioinformatics 05-10-2011, 11:06 AM
Replies: 0
Views: 2,377
Posted By Protaeus
PicardTools IlluminaBaseCallsToSam

I was going to run the subject mentioned (and probably not-oft used) tool in Picard that can demultiplex basecalls (i.e. barcodes run) into sam's or bam's. I was wondering how it deals with bcl...
Forum: Bioinformatics 03-29-2011, 08:37 AM
Replies: 2
Views: 1,247
Posted By Protaeus
454: Extremely general question

All,

I have 454 and PacBio SRA data (that are cleaned of adaptors) that I'd like to align to a reference. I've tried bwasw, but when I look at the alignments in samtools tview, they are rather...
Forum: Bioinformatics 01-19-2011, 02:46 PM
Replies: 3
Views: 2,842
Posted By Protaeus
Thanks for getting back to me. I eventually...

Thanks for getting back to me. I eventually figured it out through trial and error!
Forum: Bioinformatics 12-17-2010, 04:53 PM
Replies: 0
Views: 1,081
Posted By Protaeus
Dealing with snps at contigs junction points

Hello,

I am aligning whole genome read data against a reference in contigs with bfast as well as bwa. In both cases, I am finding a surplus of seeming snps at junction points (i.e. where N's span...
Forum: Bioinformatics 12-15-2010, 03:27 PM
Replies: 3
Views: 2,842
Posted By Protaeus
bfast with illumina mate-pair and insert size estimation

Do reads from the illumina mate-pair need to be reverse-complemented prior to alignment?

On a somewhat unrelated note, I have noted that the insert size estimation from bfast is not anywhere near...
Forum: Bioinformatics 12-09-2010, 03:38 PM
Replies: 2
Views: 4,345
Posted By Protaeus
ID'ing Uniquely Mapped Regions in BWA

I have another BWA inquiry. How can one id the uniquely mapped reads from a sam/bam generated by BWA? Thanks for any thoughts.
Forum: Bioinformatics 12-09-2010, 10:10 AM
Replies: 4
Views: 4,357
Posted By Protaeus
paired end fastq format in bwa

In some examples that I've read for using bwa to analyze paired end data, a fastq for each member of the pair is included (in other words, R1.fastq and R2.fastq). Will bwa handle paired end data that...
Forum: Bioinformatics 11-17-2010, 12:47 PM
Replies: 0
Views: 1,852
Posted By Protaeus
Info about rf vs fr with samtools or other?

I am working with Illumina GAII derived mate pair data. I am attempting to identify two things in the sequences so that I can get rid of spurious data:

1. Are the reads rf or fr. I know picard...
Forum: Bioinformatics 11-17-2010, 08:26 AM
Replies: 2
Views: 1,617
Posted By Protaeus
bfast for unmapped reads

There used to be an option to output all unmapped reads to a separate file, but it appears to no longer be an option. Are the unmapped reads printed to the sam file? If so, I assume there is an easy...
Forum: Sample Prep / Library Generation 11-01-2010, 11:04 AM
Replies: 11
Views: 4,858
Posted By Protaeus
Anyone have an update regarding...

Anyone have an update regarding successes/failures as it relates to the homemade Illumina mate pair protocol?
Forum: Bioinformatics 10-04-2010, 11:34 AM
Replies: 2
Views: 4,194
Posted By Protaeus
Assembly (velvet) of mate-pair data from Illumina

Hello,

I asked a similar question previously, but wanted to re-post to more specifically address the question of assembly (with velvet) rather than alignment.

I was writing to ask a question of...
Forum: Bioinformatics 09-30-2010, 03:09 PM
Replies: 6
Views: 3,045
Posted By Protaeus
Hey Bronnyd, No problem, though hopefully...

Hey Bronnyd,

No problem, though hopefully the responders make it clear to whom they're responding! The mate pair prep and the paired end prep are quite different. In general, I don't think you...
Forum: Bioinformatics 09-30-2010, 02:45 PM
Replies: 6
Views: 3,045
Posted By Protaeus
any clue if I would need to do so with bfast?

any clue if I would need to do so with bfast?
Forum: Bioinformatics 09-30-2010, 10:32 AM
Replies: 6
Views: 3,045
Posted By Protaeus
Illumina Mate Pair prep

Hello,

I was writing to ask a question of those who have, seemingly successfully, worked with Illumina mate pair data. I have seen other threads in which people mention that reverse complementing...
Forum: Sample Prep / Library Generation 09-28-2010, 04:41 PM
Replies: 28
Views: 11,927
Posted By Protaeus
I concur with the rumors you have heard - the...

I concur with the rumors you have heard - the Kapa kit has given me consistent and reproducible concentrations. I recommend running a qPCR on your pools as an extra QC check if you are multiplexing.
Forum: Bioinformatics 09-17-2010, 12:50 PM
Replies: 2
Views: 1,404
Posted By Protaeus
That brings up a separate but related question I...

That brings up a separate but related question I had. A lot of my recent illumina runs have been 101bp on bacterial genomes. Generally speaking, the key width for my indexes is 30. Would there be any...
Forum: Bioinformatics 09-17-2010, 10:13 AM
Replies: 2
Views: 1,404
Posted By Protaeus
bfast localalign -U option?

Hello,

What are the downsides of using the -U option at the bfast localalign step? I presume it'll be more computationally expensive, but are there things with the resulting data that would be of...
Forum: Bioinformatics 08-30-2010, 03:18 PM
Replies: 1
Views: 1,592
Posted By Protaeus
bfast gapped alignment

Naive question. I do not quite understand in what situations the postprocessing option -g would be useful (use gapped alignments when attempting to rescue pairs). Thoughts?
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