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an error occurring after run the annovar commad ,

snp annotation written 4 months ago by 543541656 • 20 • updated 4 months ago by Kevin Blighe ♦ 66k

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Annovar - SIFT prediction: Multiple transcripts, which transcript is used for scoring?

snp annotation annovar sift snp prediction written 5.7 years ago by vw • 30 • updated 5.7 years ago by dandan • 350

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Recent Replies

C: HISAT2: Question regarding providing file path to indexed genome folder by venura • 60
they are in the same directory where the job is running from. I also check the file extensions to...
A: To Translate transcriptome by h.mon ♦ 31k
[TransDecoder][1]. [1]: https://github.com/TransDecoder/TransDecoder/wiki
C: Error Bam File Is Malformed: Premature End Of File Using Gatk Tool Baserecalibra by fredjaya • 0
Thanks for the tips! Came across an identical issue and used `samtools quickcheck your.bam` to id...
C: how to identify where multi-mappers, or "non primary hits" are mapping to by genomax ♦ 91k
If you are open to trying a different aligner then you can try using `bbmap.sh` from BBMap suite....
C: how to identify where multi-mappers, or "non primary hits" are mapping to by i.sudbery ♦ 9.4k
So the short answer to this is no. As far as I'm aware, no one has written anything that can tell...
C: To Translate transcriptome by genomax ♦ 91k
Translate into protein? Use one of the EMBOSS tools. `transeq` ([LINK][1]). [1]: http://embos...
C: genome coordinates hg19 from UCSC genome browser by Alex Reynolds ♦ 31k
What UCSC visualizes in its browser uses a 1-based index, because most of us have ten digits on o...
C: genome coordinates hg19 from UCSC genome browser by Hamid Ghaedi • 500
Thanks Alex. This is why I have problem with this:) : > The UCSC Genome Browser uses two diff...
C: Funny name or unsublte hacker? by Istvan Albert ♦♦ 85k
Amusing development in the story, I wrote to ncbi asking why that folder is there, 4 days later I...
C: HISAT2: Question regarding providing file path to indexed genome folder by genomax ♦ 91k
Are the fastq files in the right spot? Are those variables correctly pointing to those files?
C: genome coordinates hg19 from UCSC genome browser by Alex Reynolds ♦ 31k
The start is actually zero; the convention is 0-based, half-open.
A: genome coordinates hg19 from UCSC genome browser by Alex Reynolds ♦ 31k
A good, generic way to do this is to get the `fetchChromSizes` tool from the [UCSC Kent utilities...

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