Hi all,
Context: I'm using the Stacks (v2.59) ref_map.pl command to analyze garden and wild samples of my species, and have aligned my...
16 results in 0.0022 seconds.
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Comparing loci across catalogs
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Really Low Bowtie2 Alignment Numbers From Demultiplex in STACKS
In STACKS, I ran process_radtags and get close to 20 million reads. They are paired-end 150bp reads.
/home/srile14/stacks-1.48/process_radtags... -
STACKS and PE Illumina Data (ddRAD)
I have a dataset from a ddRAD library (Illumina HiSeq4K, 150PE). I'm playing around with STACKS, and noticed that it has some limitations when dealing... -
ddRAD, STACKS, and Trimming
Please disregard/delete.
Last edited by Carcharodon; 07-13-2017, 04:51 PM. -
pstacks software error
Hello everyone,
can you please tell me how to resolve it .
as i am working on Stacks tool here i am trying to run pstack , cstack... -
GBS:stakcs software error in ref_map.pl
Hello Everyone,
I am currently analysing GBS data using stacks software as i ma currently facing some problem with ref_map.pl.
... -
Demultiplexing disabling FastQC
Hi all,
I got a big file of data back from the sequencing centre that worked fine when I put it through fastqc, but after demultiplexing... -
ddRADSeq data analysis for population structure (Stacks, dDocent...)
Hi all,
I'm working on marine species with no reference genome following ddRAD protocol by Peterson et al with size selection 400-600 bp....Last edited by yarinka; 08-18-2014, 12:50 AM. -
Stacks exce_velvetg not present
Hi
I am new in Stacks and running the paired tutorial available with the programm. I ran the steps till short_read_pairs.pl with almost 90% accuracy(some... -
Stacks process_radtags N in overhang
I have RADseq reads (using PSTI) where the first position in the overhang is almost invariably N. When I try to use process_radtags, it discards all of... -
RADSeq / Population Genomics with Polyploid Organisms
Hi all,
I am working with some polyploid organisms (ploidy not always known, but tetra and up) that we want to do some RADSeq / CRoPS sequencing... -
Permutation Strategies for RAD population genomics
I have a set of RAD data sampled from many individuals from several populations and I would like to calculate various population genetics statistics continuously... -
ddRADseq library variability
Hi everyone,
I'm in the process of running through the ddRADseq protocol with my samples and I've recently received the first lot of sequences... -
How to compare de novo and reference mappings in SNPs analysis?
Hello. I am a beginner in this field and I have a question, sorry if it is obvious !
In SNPs analysis (by Stacks software) with FASTQ sample... -
help! RAD, Stacks process_radtags.pl script, ambiguous RADs
I produced a single digest RAD library using Sbf-I, a rare cutter, following a variation of the Etter (2011) protocol available on Michael Miller's website...
