-
Hello Alex!
I have a question about short read mapping. I have 76bp paired-end fastq. When I using total DNA fasta as reference sequnce, uniquely mapped read % was more than 80%. In this time, howe…
-
Hi Alex and all!
I am going to handle some short sequence reads, which may be ~20bp or even shorter.
Is it still appropriate for mapping such short reads using STAR by tuning some parameters?
T…
-
Hi,
After shift and splitting bams according to fragment size, I see amongst all bam the largest bam is NulceosomeFree.bam which is expected. However, when I run estLibSize (from ChIPpeakAnno packa…
-
Hello,
I'm trying to run OPERA-MS using this command:
`perl /home/arvodnev/OPERA-MS/OPERA-MS.pl --contig-file /home/arvodnev/test_project/AssembledSR/SPAdes/contigs.fasta --short-read1 /home/arvodne…
-
Hello
I am trying to run the code:
SemiBin2 single_easy_bin -i assembly/megahit/coassembly/coassembly.contigs_renamed.fa -b mapping/bam/cobinning/*.sorted.bam -o binning/Semibin2
I think the…
-
I am following these commands. However, I am getting blank output file.
minimap2/minimap2 -x ava-pb -t8 pb-reads.fq pb-reads.fq | gzip -1 > reads.paf.gz
# Layout
miniasm/miniasm -f reads.fq reads…
-
Hello,
I have some short-read genomes that were assembled via reference mapping (different references) that I would like to align to each other. I have consensus sequences with masked reference sites…
-
# Bare Metal C++ Register Access API - AllThingsEmbedded
Introduction to memory-mapping Note: This section is introductory material for those who are not yet familiar with the concept of memory-mappi…
-
Hi,
I'm using HISAT2 to align ribosomal profiling reads (25-35nt) to a human reference. I'm getting a very large proportion of multi-mapping reads. On average, only ~7% of mapped reads were unique …
-
I am new user of STAR, and I am mapping my miRNA fastq file, and my data is 50bp, HS4000 single end run! but the number of reads unmapped and flagged as short is over 97%. Not sure why, any suggestion…