Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • standonn
    replied
    Yes, the problem was solved the following way:

    First, after demultiplexing the RAD-seq data, I ran the denovo_map of stacks. I specified "F2" as the cross (option -A). Depending on the cross that was performed choose the one corresponding to your data. I think this was my problem. I didn't choose the right cross thinking I had another type of data. Once that confusion was sorted, everything started to work.

    After running deno_map.pl I ran the genotypes program the following way:
    genotypes -b 1 -P . -r 7 -t F2 -o onemap -c

    This allowed me to get the genotypes for each marker and of each progeny sample in the onemap format.

    Then I ran onemap to build linkage groups and order the markers:
    This is what I got:
    > F2 <- read.mapmaker(file="for-onemap-analysis.txt")
    --Read the following data:
    Type of cross: f2
    Number of individuals: 95
    Number of markers: 1329
    > twopts.f2 <- rf.2pts(F2)

    > mark.all <- make.seq(twopts.f2, "all")
    > (LGs <- group(mark.all, LOD=20, max.rf=0.5))
    This is an object of class 'group'
    It was generated from the object "mark.all"

    Criteria used to assign markers to groups:
    LOD = 20 , Maximum recombination fraction = 0.5

    No. markers: 1329
    No. groups: 7
    No. linked markers: 1294
    No. unlinked markers: 35

    With this LOD/max.rf I built 7 groups (and I know this is the number of chromosome of my species). These groups contain most of the markers. I then continued the analysis: ordered the markers using the RECORD method, cleaned the map using R/QTL (with R/QTL you can remove duplicate markers and samples, remove markers/samples with a lot of missing data, look at the segregation distortion...).

    I hope this helps. Ah, I also re-ran the stacks ref_map.pl pipeline and it gave me the same result (the maps from the denovo_map.pl and from ref_map.pl are extremely similar).

    Best,
    Sophie

    Leave a comment:


  • fenduoduo
    replied
    Hi standonn,
    I have the same problem. Do you have a solution now?

    Leave a comment:


  • standonn
    replied
    Thanks for answering! I'll follow your advice and post my question on the Stacks forum. Thanks for the link!

    Leave a comment:


  • SNPsaurus
    replied
    You could write your question to the Stacks Google group (https://groups.google.com/forum/#!forum/stacks-users). Julian is pretty responsive.

    I'd say it is normal to increase the number of unlinked markers as you increase the LOD score stringency. I don't know if your numbers look typical though.

    Leave a comment:


  • standonn
    started a topic Building a genetic map from RAD-seq using OneMap

    Building a genetic map from RAD-seq using OneMap

    Dear all,

    I have some RAD-seq data from 2 parents and 97 offsprings. I would like to use this data to cluster my genomic scaffolds into linkage groups. I'm new to handling RAD-seq data and I'm not sure if what I'm doing is correct.

    For the moment I have done the following:
    - Quality Control of the RAD-seq reads
    - Demultiplexed the files
    - Mapped the RAD-seq reads to the genomic scaffolds (Bowtie2 + Samtools)
    - Ran the ref_map.pl pipeline of Stacks, specifying a "onemap" output from the program "genotypes"
    - Followed the tutorial step of OneMap (https://cran.r-project.org/web/packa...ed_version.pdf)

    Now here is where things start not working: as I increase the LOD value, I get more linkage groups but I also increase the number of unlinked markers.

    For example, with LOD=6, I get:
    > groups
    This is an object of class 'group'
    It was generated from the object "all.mark"

    Criteria used to assign markers to groups:
    LOD = 6 , Maximum recombination fraction = 0.5

    No. markers: 1342
    No. groups: 1
    No. linked markers: 901
    No. unlinked markers: 441

    With LOD=20, I get:
    > groups
    This is an object of class 'group'
    It was generated from the object "all.mark"

    Criteria used to assign markers to groups:
    LOD = 20 , Maximum recombination fraction = 0.5

    No. markers: 1342
    No. groups: 9
    No. linked markers: 225
    No. unlinked markers: 1117

    Is it normal to lose so many markers? What am I doing wrong?

    Also some groups (with LOD=20), only have 2 markers which I guess is insufficient to have a good genetic map.

    Any help or insight about building a genetic map using RAD-seq highly appreciated!

    Cheers!

Latest Articles

Collapse

  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 10:28 AM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 07:35 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-22-2024, 02:06 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-14-2024, 07:03 AM
0 responses
28 views
0 likes
Last Post seqadmin  
Working...
X