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Forum: Bioinformatics 10-18-2017, 10:12 AM
Replies: 13
Views: 6,888
Posted By etwatson
I'm going to bump this thread to mention to...

I'm going to bump this thread to mention to mention that BAMs merged with samtools merge will not produce output unless the -c flag is provided to combine @RG headers with colliding IDs - if...
Forum: Vendor Forum 02-17-2016, 10:06 AM
Replies: 2
Views: 2,985
Posted By etwatson
Congratulations. The nextRAD method looks...

Congratulations. The nextRAD method looks promising for our research. Our model organism for evolutionary research, Tigriopus californicus, is very small and DNA extraction yields have proven to be...
Forum: Bioinformatics 03-06-2015, 10:37 AM
Replies: 14
Views: 8,131
Posted By etwatson
Now I'm confused. I am using the -f4 flag to...

Now I'm confused. I am using the -f4 flag to extract unmapped reads. Are unmapped reads altered?
Forum: Bioinformatics 02-26-2015, 05:55 PM
Replies: 8
Views: 6,154
Posted By etwatson
Hey Daren!! This looks like a pretty good idea...

Hey Daren!! This looks like a pretty good idea you have worked out.
Forum: Bioinformatics 02-26-2015, 05:41 PM
Replies: 14
Views: 8,131
Posted By etwatson
Ok, after my coffee break, I decided to lean on...

Ok, after my coffee break, I decided to lean on my awk crutch.

This did the job:
samtools -f4 file.srt.bam | awk 'BEGIN{OFS="\n"}{print "@"$1,$10,"+",$11}'> reads.fastq
Forum: Bioinformatics 02-26-2015, 03:01 PM
Replies: 14
Views: 8,131
Posted By etwatson
picard - samtools discrepancy

I am also having this issue, and it appears to be a headache for many people.

I am not interested in paired-end information, since I am comparing unmapped reads to a library of de-novo assembled...
Forum: Genomic Resequencing 01-13-2015, 11:55 AM
Replies: 1
Views: 3,519
Posted By etwatson
plink2 to EIGENSOFT .geno conversion

Hi all,

I have used plink2 for my project, and now have a database of .ped, .map, .bim, .fam, etc... files. I am interested in trying a new program to perform a PCA analysis for population...
Forum: Bioinformatics 10-31-2013, 03:49 PM
Replies: 16
Views: 3,736
Posted By etwatson
That makes sense from a performance point of...

That makes sense from a performance point of view. I began to write a script to save the unpaired(orphaned) reads, and it looks like there are plenty of scripts out there that ensure proper pairing...
Forum: Bioinformatics 10-31-2013, 01:43 PM
Replies: 16
Views: 3,736
Posted By etwatson
Why would bwa try to pair two reads that have...

Why would bwa try to pair two reads that have different names just because they are on the nth read in a list? I'm having the same problem, with my pe read names not sorting to same line. I traced...
Forum: Bioinformatics 10-31-2013, 01:16 PM
Replies: 1
Views: 2,156
Posted By etwatson
Problem solved. I ran fastq_quality_trimmer...

Problem solved.

I ran fastq_quality_trimmer on my raw reads, and the output PE files did not match up, causing large inferred insert sizes.
Forum: Bioinformatics 10-31-2013, 12:19 PM
Replies: 1
Views: 2,156
Posted By etwatson
BWA insert size distribution too large

I'm trying to align pe reads to our reference genome (Tribolium), which has a couple thousand unmapped contigs. The reference has 10 chromosomes , each around 10 - 30 Mb in size, while the rest of...
Forum: Bioinformatics 10-21-2013, 03:11 PM
Replies: 57
Views: 36,675
Posted By etwatson
btmb, I got your edited script to run today,...

btmb,

I got your edited script to run today, thank you. However, it prints nothing out to the created files. I get the following error.


Here are the corresponding lines in the script:

...
Forum: Bioinformatics 08-14-2012, 09:23 AM
Replies: 3
Views: 2,233
Posted By etwatson
Greetings all, I'm guessing that nobody else has...

Greetings all, I'm guessing that nobody else has encountered this error. Can anyone help me trouble shoot it? What is a buffer overflow, and what can I do to get bwa working?
Forum: Bioinformatics 06-20-2012, 03:08 PM
Replies: 3
Views: 2,233
Posted By etwatson
1.) Version: 0.5.9-r16 2.) Yes 3.) Yes 4.)...

1.) Version: 0.5.9-r16
2.) Yes
3.) Yes
4.) see image showing bwa start and crash (I'll have to upload this later)
5.) bwa sampe <ref.fasta> <46sa1.sai> <46sa2.sai> <46sa1.fastq> <46sa2.fastq> >...
Forum: Bioinformatics 06-20-2012, 09:23 AM
Replies: 3
Views: 2,233
Posted By etwatson
Buffer overflow when aligning paired-end reads with BWA

Greetings folks. I'm trying an alignment of paired-end reads with bwa, and the program is crashing with a buffer overflow error. Here is the readout:
...
...
[bwa_sai2sam_pe_core] print...
Forum: Bioinformatics 06-08-2012, 02:56 PM
Replies: 8
Views: 7,349
Posted By etwatson
I'm trying to build a reference sequence and I...

I'm trying to build a reference sequence and I have gff3 files for all contigs. It seems like CLC doesn't like the gff3 files, because I don't see any annotations when the plugin has run. Do I need...
Forum: Illumina/Solexa 06-04-2012, 08:31 AM
Replies: 1
Views: 2,338
Posted By etwatson
I am also having this issue and would appreciate...

I am also having this issue and would appreciate the response.
Forum: Introductions 06-04-2012, 08:24 AM
Replies: 0
Views: 1,179
Posted By etwatson
Howdy!

Greetings from Texas. I'm a PhD candidate in the field of evolutionary genetics, and I am here to do some population genomics with Illumina HiSeq data. I already have my reads, and now I will be...
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