User: human_genomeXXX
human_genomeXXX • 10
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Posts by human_genomeXXX
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... for mutation profiling, thx ...
written 4.0 years ago by
human_genomeXXX • 10
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... There are no chromosomes in M tuberculosis like in human, as far as i remember Microbiology medschool course.... However, Mycobacterium tuberculosis has circular chromosomes of about 4,200,000 nucleotides long. Genome size is 4 million base pairs, with 3,959 genes; 40% of these genes have had their ...
written 4.0 years ago by
human_genomeXXX • 10
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... I have .sam and .bam alignments to paired fastqs files, thank you ...
written 4.0 years ago by
human_genomeXXX • 10
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... Pilon and BBMap generate VCf file where are chromosome names seem to be absent, how to fix that?
Reference is a standard tub. genome. Aligners are BWA and Snap, BBmap, tried all of them.
i s it necessary to use gff3 file somehow?
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written 4.0 years ago by
human_genomeXXX • 10
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Need help to choose 2-3 genome annotation software from the list at https://omictools.com/genome-annotation-category
Input will be a VCF files generated from the Pilon, BBMap, GATK and NextGene. Please do not propose SNPEff and VCFAnnotator. Objects of research --- M.Tuberculosis, E. coli, Staf. ...
written 4.0 years ago by
human_genomeXXX • 10
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... How to download tuberculosis reference using the last version of SNPEff?
I have tried java -jar snpEff.jar download -v m_tuberculosis.reference ...
written 4.0 years ago by
human_genomeXXX • 10
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... There is a "cant find chromosome error" in SNPEff output see VCF`s headers https://www.biostars.org/p/234735/#234856. What
exactly commands can fix that? thank you ...
written 4.0 years ago by
human_genomeXXX • 10
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... How to preprocess, normalize, decompose a VCF file before inputting to the SNPEff? Heard, people use -sed and -grep to process VCFs somehow. ...
written 4.0 years ago by
human_genomeXXX • 10
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... I post the other one, it looks unhealthy ---
##fileformat=VCFv4.2
##BBMapVersion=36.86
##ploidy=1
##rarity=1.00000
##minallelefraction=0.10000
##reads=789372
##pairedReads=789372
##properlyPairedReads=562846
##readLengthAvg=90.982
##properPairRate=0.71303
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written 4.0 years ago by
human_genomeXXX • 10
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... ##fileformat=VCFv4.1
##fileDate=20170202
##source="Pilon version 1.21 Fri Dec 9 16:44:44 2016 -0500"
##PILON="--genome H37Rv_reference.fa --frags file.sorted.bam --output pilon_output.pilon --vcf"
##reference=file:/home/mat29/Desktop/Ready_Genomics_software/H37Rv_reference.fa
...
written 4.0 years ago by
human_genomeXXX • 10
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