Activity for daniel andergassen
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daniel andergassen posted a comment on ticket #1
Hi Carol, We fixed the issue with Samtools, just click on the link to download an updated version of Allelome.PRO that works with the newest version of samtools (tested for samtools v1.3 and v1.5). https://sourceforge.net/u/fpauler/allelomepro/ci/master/tarball All the best, Daniel Am Sa., 22. Sep. 2018 um 07:02 Uhr schrieb Florian Pauler fpauler@users.sourceforge.net: Hi, Just to clarify: C57Bl/6J and C57Bl/6NJ are not genetically identical - for known differences see https://www.jax.org/strain/005304....
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new version that works with samtools1.x
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fix to work with latest samtools version
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Hi Carol, We will upload an updated version of Allelome.PRO next week that runs with the new version of Samtools. I will update you when you can download it. Daniel Am Fr., 21. Sep. 2018 um 09:19 Uhr schrieb Carol Edwards cae28@users.sourceforge.net: Thanks Daniel, we are a bit reluctant to change our version of SAMtools to an earlier one. Is there are point in the pipeline where we can specify a different version of SAMtools rather than using the PATH environments one? Carol On 21-09-2018 13:20,...
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Hi Carol, I just run the testdata and got the same error by using samtools (v1.5). Than I was running the pipeline again using the suggested samtools version 0.1.19 and it worked! Don't forget to also load R in your System which is needed later in the script! Good luck and let me know if it works! All the best, Daniel Am Fr., 21. Sep. 2018 um 07:06 Uhr schrieb Carol Edwards cae28@users.sourceforge.net: Dear Daniel, Thanks for your help. We are trying to run the test data but we keep getting the following...
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Hi Carol, Only the numbers are required. Just use the number 8 for C57Bl/6J which is listed as C57Bl/6NJ. These two strains should be genetically identically, the only difference is that they were hosted in different mouse facilities N for NIH and J for Jackson lab. command: sh createSNPbedfile.sh path/mgp.v3.snps.rsIDdbSNPv137.vcf outputfile.bed Also remember the order of the strains you use to generate the SNP file, which is important later in the Allelome.PRO pipeline when you fill out the configs!...
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