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Forum: Illumina/Solexa 12-19-2018, 04:58 AM
Replies: 0
Views: 772
Posted By mhmtgenc
Can I see the detailed information of off-target reads of sequencing on NextSeq 500?

I would like to see the off-target read details of the run on NExtSeq 500 with TruSeq Rapid Exome kit?

I know that Ihave lots of reads but I lose too many of them as saying not mapped or...
Forum: Illumina/Solexa 12-17-2018, 10:42 PM
Replies: 3
Views: 911
Posted By mhmtgenc
Thanks for the answer. So could you suggest...

Thanks for the answer. So could you suggest anything with that? Because I have been following the exact steps of the kits checklist guide.
Forum: Illumina/Solexa 12-17-2018, 03:15 AM
Replies: 3
Views: 911
Posted By mhmtgenc
Low Exome Coverage with Truseq DNA Exome and NextSeq 500 workflow?

Dear All,

I studied a whole exome with Truseq DNA Exome (2x75 and suitable High output kit) on NextSeq 500.. AFter sequencing I got around 46 million reads per sample and 42 million of these were...
Forum: Bioinformatics 12-07-2018, 01:11 AM
Replies: 0
Views: 535
Posted By mhmtgenc
Truseq Rapid Exome TArget Bed file's Gene Names?

İs there a way to get gene names of the Truseq Rapid exome Target Bed file whihc only includes target coordinates?
Forum: Bioinformatics 08-07-2018, 03:22 AM
Replies: 4
Views: 1,815
Posted By mhmtgenc
So how coul I be able to get a BED file or...

So how coul I be able to get a BED file or prepare it by myself? Could you give me a clue or a tutorial of this. Cause I have trouble on this. I know this is hard to expalin it here but can I get any...
Forum: Bioinformatics 08-07-2018, 12:24 AM
Replies: 4
Views: 1,815
Posted By mhmtgenc
How to get a report like stuff of a bam file how many percent of the exons are cover

Dear Collegues,

Lets say I have a miseq run and have the .bam file from the squencer and I would like to know how many percent of the exons (specific genes) are coverred in these .bam files?

Is...
Forum: Bioinformatics 04-11-2018, 02:37 AM
Replies: 1
Views: 707
Posted By mhmtgenc
No mutations in BAM (IGV) but a mutation in final VCF?

I use GATK 4.0 for the variant calling pipeline. my steps involve MarkDuplicates, BaseRecalibration, ApplyBaseRecalibration and HaplotypeCaller. When I check in a loci there is no mutation in the...
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