Activity for Allelome.PRO
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Allelome.PRO updated /readme.txt
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Florian Pauler modified ticket #1
createSNPbedfile.sh
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createSNPbedfile.sh
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2 problems were solved in this ticket: 1) SNPs from C57Bl/6JN can be safely used for any C57Bl/6 strain 2) using bedtools 2.27 solved the problem of empty output files
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Carol Edwards posted a comment on ticket #1
Hi Florian, I have hopefully sent you the dropbox link with the file in it Carol On 24-09-2018 12:42, Florian Pauler wrote: Hi Carol, Sorry for my sloppy typing - of course it is "intersectBed". Could you provide me the compressed output folder via dropbox or similar ? - in this way I can perhaps trace back the error. best, Florian [TICKETS:#1] [1] CREATESNPBEDFILE.SH STATUS: open MILESTONE: 1.0 CREATED: Thu Sep 20, 2018 08:43 AM UTC by Carol Edwards LAST UPDATED: Mon Sep 24, 2018 10:42 AM UTC OWNER:...
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Hi Carol, Sorry for my sloppy typing - of course it is "intersectBed". Could you provide me the compressed output folder via dropbox or similar ? - in this way I can perhaps trace back the error. best, Florian
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Hi Florian, we can run bedtools intersect from the command line but intersectbed does not exist in version 2.26. we can run intersectBed which I believe is the same as intersect Carol On 24-09-2018 11:42, Florian Pauler wrote: Hi Carol, Just to make sure that your environment is correctly configured: Have you installed samtools, bedtools and perl on your system? Can you run intersectbed (from the bedtools suite) from the command line? best, Florian [TICKETS:#1] [1] CREATESNPBEDFILE.SH STATUS: open...
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Hi Carol, Just to make sure that your environment is correctly configured: Have you installed samtools, bedtools and perl on your system? Can you run intersectbed (from the bedtools suite) from the command line? best, Florian
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On 23-09-2018 16:46, daniel andergassen wrote: 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 [4] All the best, Daniel Dear Daniel, Thanks for that. The samtools issue has resolved but I still get no SNP info back from the pipeline. in the info.txt no SNPs were discovered Read counts:...
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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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new version that works with samtools1.x
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fix to work with latest samtools version
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Hi, Just to clarify: C57Bl/6J and C57Bl/6NJ are not genetically identical - for known differences see https://www.jax.org/strain/005304. However most of the SNPs mapped using C57Bl/6NJ will be identical in C57Bl/6J. Importantly the Allelome.PRO pipeline does identify correctly annotated SNPs by using reciprocal crosses and therefore it is safe to use C57Bl/6NJ for any C57Bl/6 strain. best, Florian
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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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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, daniel andergassen wrote: 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...
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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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Dear Daniel, Thanks for your help. We are trying to run the test data but we keep getting the following error messages start read trimming for sample 1 start read trimming for sample 2 start read trimming for sample 3 start read trimming for sample 4 [E::hts_open_format] fail to open file './test_run/results//2018_09_21_MEF_CF_1_Igf2r_cl_MEF_CF_2_Igf2r_cl_MEF_FC_1_Igf2r_cl_MEF_FC_2_Igf2r_cl_RefSeq_annotation_Igf2r_cl.bed_1_1/debug/fc1_MEF_CF_1_Igf2r_cl/BAM_trim/trimmed_s.bam' samtools view: failed...
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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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createSNPbedfile.sh
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Christoph Dotter committed [34d416]
Updated createSNPbedfile.sh to detect FI column...
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Initial commit
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