User: toralmanvar

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toralmanvar730
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Posts by toralmanvar

<prev • 164 results • page 1 of 17 • next >
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Comment: C: bcl to fastq
... yes, you can download bcl2fastq from [here][1] and can install it offline. [1]: https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html ...
written 29 days ago by toralmanvar730
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... Usually, in case of incompatibility of reference genome you end up with [this][1] kind of problems. But this not the case here. But give a try using reference genome from this [link][2] for 1000G VCF files. [1]: https://software.broadinstitute.org/gatk/documentation/article?id=11012 [2]: ftp:/ ...
written 29 days ago by toralmanvar730
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... That's unusual. You might have gone through [this][1] GATK forum, but if not, see whether it can be useful to you. [1]: https://gatkforums.broadinstitute.org/gatk/discussion/8946/qd-annotation-not-found-variant-recalibrator-error ...
written 29 days ago by toralmanvar730
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Comment: C: how many files are generated after sorting of .bam file ?
... Check [this][1] [1]: https://www.biostars.org/p/289378/ ...
written 4 weeks ago by toralmanvar730
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... Have you validated the input VCFs with ValidateVariants? ...
written 4 weeks ago by toralmanvar730
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Comment: C: The evidence of the gene annotation
... According to me, both can work as evidence. But in the case of blastx result, those are only annotated sequences which you consider, on the other hand latter gives you a complete set of proteins. ...
written 4 weeks ago by toralmanvar730
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Comment: C: Can I use VarScan for tumor_time2/tumor_time1 CNA and SNP calling?
... https://www.biostars.org/p/243387/ ...
written 4 weeks ago by toralmanvar730
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Comment: C: bcl to fastq
... Though it is not the proper solution. I think you can try taking undetermined reads left after demultiplexing of 3 samples as data for your 4 sample. If you have added PhiX Control then you can map undetermined reads to PhiX genome and can work with remaining data. ...
written 5 weeks ago by toralmanvar730
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Comment: C: Assembly gene prediction/annotation
... I think you should frame your question to include word "plant mitochondria", so that people can search your post using those key words. ...
written 5 weeks ago by toralmanvar730
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Comment: C: Assembly gene prediction/annotation
... That's for assembly and not annotation. ...
written 5 weeks ago by toralmanvar730

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