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Hi,
Is there a reason why freebayes reports this SNP position as homo instead of hetero?
It has 3406 T and 3025 C , no quality or strand-bias problems (or so it seems to me), it is reported as a v…
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freebayes -F 0.001 -n 2 -X -u -f ../hg19/ucsc.hg19.fasta IonXpress_042_rawlib.bam >42.vcf
why write output like this?
CAC===>CTC so why not A ====> T
chr7 140453135 . CAC CTC 1.18227…
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Hi,
I used two different methods to do base quality correction for the sequenced data, and the depth information was consistent. The results of QR and QA were a little different, but the genotypes o…
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Mentioned in iwc chat, I'm experiencing linting format2 workflows. I'm testing with [one of the GTN workflows](https://github.com/galaxyproject/training-material/blob/main/topics/assembly/tutorials/de…
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Hi all,
I recently used prokka to annotate a bacillus species. I noticed there were more CDS called by prokka than what NCBI estimates this organism should have. Prokka annotated 5050 CDS, whereas …
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I see that Ion-Torrent data can be input directly using a BAM file, but it doesn't look like this is an option for other platforms, e.g. Illumina data.
I'm working on a mapping/extraction/assembly…
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I'm trying to get a pipeline working with single-end reads sample as an input. The pipeline has been defined but when a single-end reads sample is added to the cart and the pipeline is selected, the p…
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Dear developers,
Is there a way to pass the spades flag "--iontorrent" to your pipeline or are only illumina reads allowed ?
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Hello.
I'm currently working with maftools to visualize IonTorrent NGS data which contains information about hotspot variants we've selected (i.e. ~1,400 variants).
The problem is whenever I t…