User: NGSCanBioinf

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NGSCanBioinf10
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Posts by NGSCanBioinf

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Answer: A: Using vcfanno to annotate VCF file with CADD1.6 "tsv.gz" files
... Came across this very relevant link: http://brentp.github.io/vcfanno/examples/cadd/ I followed the instruction and it runs with the following output vcfanno version 0.3.2 [built with go1.12.1] see: https://github.com/brentp/vcfanno ============================================= ...
written 3 days ago by NGSCanBioinf10
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Using vcfanno to annotate VCF file with CADD1.6 "tsv.gz" files
... Hello, I am trying to use vcfanno tool to annotate my query VCF file with the CADD v1.6 files that I have installed. These files come as "tsv.gz" files with the following format which resembles neither VCF (where I would use the "fields=" option) nor BED (where I would use the "columns=" option): ...
annotation vcfanno written 4 days ago by NGSCanBioinf10
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Comment: C: Padding of exonic intervals
... Thank you for your reply. I have seen both per base coverage output which makes a very long file and also per interval coverage output, I was referring to the latter in this case. ...
written 9 days ago by NGSCanBioinf10
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Padding of exonic intervals
... Hello, I am running WES samples through gatk based NGS pipeline. I have a BED file limited to exonic intervals. When I use this BED file the variant calling is limited to exonic intervals which saves time but I am concerned that some splicing variants may be excluded. One solution would be to padd t ...
next-gen written 9 days ago by NGSCanBioinf10
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Comment: C: adapter sequence positions
... Great, thanks again for good points! ...
written 13 days ago by NGSCanBioinf10
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Comment: C: adapter sequence positions
... Thanks, these are good points. I will look into the scripts you mentioned. We have received these files from collaborators so may need to check with them, but in general is it recommended to check if the reads are reverse complemented for any fastq file received from sequencing centres? and if they ...
written 13 days ago by NGSCanBioinf10
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Comment: C: adapter sequence positions
... Thank you, these are WGS samples, and the overrepresented sequence is identified as "TruSeq Adapter, Index 18" by Fastq which reports 101,779 of them (i.e. 0.16%) in the file. From rough visual inspection, 90% of these have the adapter sequence in the beginning (i.e. left side) of the sequence. Trim ...
written 13 days ago by NGSCanBioinf10
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adapter sequence positions
... Hi, from my understanding the adapter sequences can only occur on the 3' side of the sequencing reads if there is a read through. Does this mean that when you open a Fastq file (either R1 or R2) to inspect, you should see the majority of them on the right side of the file? In my Fastq files the majo ...
sequence written 13 days ago by NGSCanBioinf10 • updated 13 days ago by JC11k

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Scholar 3 days ago, created an answer that has been accepted. For A: Using vcfanno to annotate VCF file with CADD1.6 "tsv.gz" files

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