Entering edit mode
7.2 years ago
human_genomeXXX
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10
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?
Do you have alignments to all of the chromosomes?
A gff3 file is useless here.
I have .sam and .bam alignments to paired fastqs files, thank you
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 function characterised, with possible function postulated for another 44%. Within the genome are also six pseudogenes...
Right, so perhaps show a brief example of what you're observing, since you seem to be writing in a self-contradictory manner.
It can't answer you anymore....
Can't say I hadn't thought about suspending the account myself :P
I suspended the next one :p It was named after you: gotohelldevon
Just do it, let them file a complaint later, if they are human :D
The Vassialk bot is back.
What's the point of a bot like this?
I have no clue, its just not worth to try to interact with it. I believe it is trying to level up and get some votes somehow so it can do more.
If you see the key words: tuberculosis, SNP, VCF, Nextgene,..., "tried all of", "don't recommend", and then the bot hits the max posts cap having all the words in the bag, just suspend it, no questions asked.