-
I want to use MGcounts's ability to find communities of multimapping features, on some sequencing data of synthetic constructs. I have made a fasta, aligned to it, and made a fake gtf file with all of…
-
Working with several different sequencing runs of various qualities I am trying to develop intuition for what reasonable quality filtration parameters are in the function `filterAndTrim`. The relevant…
-
I saw in #7 that for amplicon-awared variant calling, the BED file need to have 8 columns storing both the primer and insert positions. However, the BED file that comes with the manufacturer's target…
-
Hi,
Thanks for the tutorial!
I would like to determine the co-occurrence between two different composition from the same samples (I used two different amplicon sequencing approach from the same sa…
-
Currently, PoolListHandler.get throws a 500 error if it is passed a pool type that it doesn't recognize. This is as it should be :) However, one of the places this get is used is within an ajax call…
-
Hi,
We recently implemented masking using this table. We realised that certain sites might only require masking when using a particular primer set as we are seeing sites for lineage defining mutati…
-
Hi Bram,
I am using RTCR to identify the TCR repertoire from amplicon sequencing. I have some more question abouts the output result.
1) how can get the mapping rate for the fastq reads (MiSeq, …
-
when I use vsearch for amplicon sequencing data analysis, I have installes vsearch
when I use it, something wrong happended:
`ubuntu@ip-172-31-14-112:~/LC$ time vsearch ‐‐usearch_global seq18s-…
-
"Whole-genome sequencing and targeted amplicon capture" says:
> "Do not mark duplicates in the BAM files for samples sequenced by this method"
However, in the BAM file preparation, it is writt…
-
"Latest mapping file downloaded is empty, however AGP mapping files in the past were downloaded with no trouble."
Review download buttons from existing plates, etc. and ensure content is downloadab…