Forum: Bioinformatics
10-18-2017, 10:12 AM
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Replies: 13
Views: 6,888
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...
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Forum: Vendor Forum
02-17-2016, 10:06 AM
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Replies: 2
Views: 2,985
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...
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Forum: Bioinformatics
03-06-2015, 10:37 AM
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Replies: 14
Views: 8,131
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Forum: Bioinformatics
02-26-2015, 05:55 PM
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Replies: 8
Views: 6,154
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Forum: Bioinformatics
02-26-2015, 05:41 PM
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Replies: 14
Views: 8,131
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Forum: Bioinformatics
02-26-2015, 03:01 PM
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Replies: 14
Views: 8,131
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...
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Forum: Genomic Resequencing
01-13-2015, 11:55 AM
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Replies: 1
Views: 3,519
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...
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Forum: Bioinformatics
10-31-2013, 03:49 PM
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Replies: 16
Views: 3,736
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...
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Forum: Bioinformatics
10-31-2013, 01:43 PM
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Replies: 16
Views: 3,736
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...
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Forum: Bioinformatics
10-31-2013, 01:16 PM
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Replies: 1
Views: 2,156
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Forum: Bioinformatics
10-31-2013, 12:19 PM
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Replies: 1
Views: 2,156
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...
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Forum: Bioinformatics
10-21-2013, 03:11 PM
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Replies: 57
Views: 36,675
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:
...
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Forum: Bioinformatics
08-14-2012, 09:23 AM
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Replies: 3
Views: 2,233
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Forum: Bioinformatics
06-20-2012, 03:08 PM
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Replies: 3
Views: 2,233
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> >...
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Forum: Bioinformatics
06-20-2012, 09:23 AM
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Replies: 3
Views: 2,233
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Forum: Bioinformatics
06-08-2012, 02:56 PM
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Replies: 8
Views: 7,349
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...
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Forum: Illumina/Solexa
06-04-2012, 08:31 AM
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Replies: 1
Views: 2,338
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Forum: Introductions
06-04-2012, 08:24 AM
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Replies: 0
Views: 1,179
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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