Carol Edwards

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:...

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...

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:...

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...

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...

createSNPbedfile.sh