ema
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arshajii
Fast & accurate alignment of barcoded short-reads
Looking over the output of some test [haplotag] data, column 9 (`TLEN`) is showing `0` for many alignments, even if the alignment positions are present. Example record: ``` A00470:481:HNYFWDRX2:1:2239:18150:28354_A61C72B93D96_GAACGACTACCACAG 113...
During testing of #51 I noticed that haplotag barcodes were not the same when comparing input to output of `ema align`. For example this is the read `A00814:267:HTMH3DRXX:2:1101:3197:1016` in the...
I have noticed that in some instances not all reads that are use as input are included in the output from `ema align`. I have included some test data (see...
Hello, I use haplotagging data with the EdHarry ema fork and have been trying to use the LEVIATHAN variant caller, which relies on split read information to call variants. My...
Noticing that the default read length limit is 200, I changed the max_read_length to be 1000 to force the program to work. But I'm not sure if it will still...
I am running ema on haplotagged sequences and the preprocessing seems to be done correctly. But while running `parallel --bar -j10 "ema align -t 4 -d -r $ref_genome -p 10x...
I find the definition of profiles for different sequencing technologies in Techs.h: ``` static PlatformProfile profiles[] = { {.name = "10x", .extract_bc = extract_bc_10x, .many_clouds = 0, .dist_thresh = 50000,...
Dear author, I would like to use Emerald to align my 10X genomics reads to a reference. After reading the README and the issues page I am confused about the...
I have been running ema (version 0.6.2) on reads in the longranger basic FASTQ format (BX:Z in header). I pipe the output directly to `samtools sort`. My command looks something...
Default settings has read density optimization switched off, while the rdo is highlighted as an important feature in the publication. Why?