magicblast issues

Mistakes on small introns

3

Hi，magicblast take small introns (peaks at 23 bp) in my genome as deletions, and I cannot find any way to solve it, do you have any great suggestions?

sunriseTM

Error while running magicblast

1

Hi everyone, I find my individual samples paired-reads against an 18S database using the following function by following the tutorial at https://astrobiomike.github.io/amplicon/16S_and_18S_mixed#evaluating-the-outcome: for sample in $(cat samples.txt) do printf "\n...

pablomics-star

Use magicblast to map an experiment in the SRA reporitory

12

Hi, I have used magicblast version 1.4.0 and 1.5.0 in the past to map a query to experiments in the SRA repository. I have now installed the latestmagicblast version and...

sabina-llr

Use NCBI SRA repository ( NCBI Magic-BLAST RNA-seq mapping tool)

9

Hello how are you! I'm trying to use the NCBI Magic-BLAST tool RNA-seq mapping tool, but I'm not getting it. I followed the tutorial available on NCBI (https://ncbi.github.io/magicblast/cook/sra.html). Firstly I...

joseailtoncruz

Meaningful MAPQ values would be excellent.

4

Hi all, I am trying out Magic-BLAST for mapping short-reads, and may want to test it in various pipelines. I noticed, however, that the MAPQ field in the SAM output...

JohnUrban

problems with really short exons (10-6 bp)

4

Dear all, I am surprised how well the program is working. However, I have a question. Is it possible to fine toon the aligner in order to detect smaller exons...

HegedusB

-fr and -rf flags for strand specific RNA-seq

3

Hello, I am mapping some paired-end strand-specific RNA-seq. This data maps logically with STAR, with the majority of reads in sense with their transcript. However, this is not the case...

asethi-1

taking longer and using more memory than expected

2

Dear all, I am trying to use this tool for mapping RNAseq reads to a plant reference genome. I have 50 libraries with around 2.5Gb of data in each (2...

jdmontenegro