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data orgin #1
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Hi, Thanks for your interests. The tripsacum fasta file was generated via ANGSD, extracting consensus sequence from bam files. Please refer to "angsd.abba-baba.sh" for instructions. |
Hi @lepisorus , |
The coverage matters when extracting the consensus sequences. The tripsacum
data I used was from Hapmap2, see Hufford et al. 2012 Nature Genetics.
We chose Mexican Lowland as the reference population, because that is the
population did not receive introgression from mexicana .
…On Mon, Nov 20, 2017 at 7:21 PM, conniecl ***@***.***> wrote:
Hi @lepisorus <https://github.com/lepisorus> ,
Thanks for your kindly explanation, I used the command as you show in "
angsd.abba-baba.sh" , by using the unique map bam file and raw bam file,
the result is very different, may be caused by the coverage? *Is there
any suggestion about the bam file?* Since I'm confused about it.
Besides, I also try to caculate the fd_introgression based on your
scripts, but *why you choose Mexican lowland as the reference
population(P1), instead of other landrance?* And thanks again
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Li Wang
Postdoctor Research Associate
Department of Ecology, Evolution and Organismal Biology
Iowa State University
Website: lepisorus.github.io
|
Hi, Wang @lepisorus,
I want to calculate the D statistic as you show in the script
Dstatistics/abba-baba.sh
, but I'm confused about the Tripsacum.fa you use as the ancestral genome, since Tripsacum do not have a reference genome ? And how to get the Tripsacum.fa? Sincerely hope can get your advice, and thanks in advance.
/data004/software/GIF/packages/ANGSD/0.614/angsd -doAbbababa 1 -blockSize 1000 -anc /home/lwang/lwang/SRA/Tripsacum/Tripsacum.fa -doCounts 1 -bam ${BAMLIST} -uniqueOnly 1 -minMapQ 30 -minQ 20 -minInd 3 -P 8 -checkBamHeaders 0 -rf /home/lwang/lwang/SRA/scaffoldNamesWithData.txt -out ${OUTFILE}
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