User: tarekzakaria.badr

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Posts by tarekzakaria.badr

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Gatk Mutec2 germline resources for mouse
... unfortunately i couldn't find an AF germline resource suitable for Mutec so far. i have some normal matches though so i tried to filter through them and PON file. another strategy i am considering is calling also through varscan and samtools and gather common variants from all three pipelines but i ...
written 4 months ago by tarekzakaria.badr30
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Comment: C: Using GATK4 Mutect2 on mouse data, need a genome snp reference
... Hi, i am facing the same problem you have too as i am analzsing tumor samples for b6 mice and don't have matched normals for all my samples. Could you find a germline resource or PON compatible with b6 mice? Also as i understood the --dpsnp option is useless in GATK4 so i couldn't find a way so far ...
written 4 months ago by tarekzakaria.badr30
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Comment: C: Gatk Mutec2 germline resources for mouse
... thanks for your reply, i have matched normal for some of my samples, but Mutec2 suggests running the variant calling also with the germline Allele frequency resource which i couldn't find for mm10. Do you know where to find this resource for mm10 or if it would affect the final called variants in a ...
written 4 months ago by tarekzakaria.badr30
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Gatk Mutec2 germline resources for mouse
... Hi everyone, i am analyzing mouse exome data with mutec2 for somatic variants detection. I am a bit stuck with the germline resources, couldn't find one for mm10. I have used the sagner provided snps and indels for the known sites in Baserecalibator. Is it possible to used them too for the germline ...
gatk sequencing mm10 written 4 months ago by tarekzakaria.badr30 • updated 4 months ago by h.mon27k
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Comment: C: Can a normal tissue sequence be used for various tumor samples in Varscan Somati
... Thanks for your reply. I know it's very little but unfortunately i received the sequences after they have ended the experiments. Following your advice I will then run this normal tissue with the other tumor samples as a Normal/Tumor pair. I also have found SNPS and indels VCF files for mm10 and will ...
written 7 months ago by tarekzakaria.badr30
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Can a normal tissue sequence be used for various tumor samples in Varscan Somatic or GATK MuTect2?
... I have exome sequencing data from tumor samples from mice with only one of them has tumor/normal tissue sequence. All the mice share the same genetic background, bred together and i believe they come from the same mother (not 100% sure about the same mother though). I have aligned them sequences us ...
gatk varscan mutect2 written 7 months ago by tarekzakaria.badr30 • updated 7 months ago by Charles Warden7.2k
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Comment: C: Is Dell Precision mobile workstation suitable for bioinformatics/NGS analysis
... Thanks for your feedback. My idea is to run 2-3 samples (Human exome or RNAseq) per time just to be able to modify the scripts before running them on a cloud or something, and also to be able to handle R easier when dealing with large files. Do you think The ECC ram would make a big difference? beca ...
written 7 months ago by tarekzakaria.badr30
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Is Dell Precision mobile workstation suitable for bioinformatics/NGS analysis
... Hey everyone, Since i am moving a lot i was looking to get a mobile workstation to do some initial script editing while traveling and trying with few samples before applying it to the whole projects. The data we are dealing with are mostly RNAseq, and some tumor exome seq samples. some other chipse ...
ngs worksation laptop rna-seq linux written 7 months ago by tarekzakaria.badr30 • updated 7 months ago by genomax70k
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Is it possible to detect somatic SNVs from C57BL/6 tumor samples WXS without normal tissue control?
... Hi everyone, i am a little bit new to whole exome seq analysis and did it only once before for human samples using bwa and Gatk pipeline and now I have whole exome sequencing data from tumor samples for C57BL/6 mice ( Gut tumor samples 3 wild type vs 3 KO). Unfortunately the mice aren't avialabe a ...
next-gen alignment snv sequencing written 10 months ago by tarekzakaria.badr30 • updated 10 months ago by igor8.1k
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Comment: C: mice whole Exome sequencing Analysis
... Thanks a lot for your feedback and sorry for the late reply. That's an interesting pipeline. i used GATK before for normal human exome and found it convenient. A small question regarding the pipeline (sorry if it seems naive but i am really new to tumor research). We have tumor samples from the two ...
written 11 months ago by tarekzakaria.badr30

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