Tag: samblaster
Leishmania genetic exchange is mediated by IgM natural antibodies
Rapaka, R. R. et al. Conserved natural IgM antibodies mediate innate and adaptive immunity against the opportunistic fungus Pneumocystis murina. J. Exp. Med. 207, 2907–2919 (2010). Article CAS PubMed PubMed Central Google Scholar Boehm, T., Iwanami, N. & Hess, I. Evolution of the immune system in the lower vertebrates. Annu….
GenomicStar hiring Bioinformatics Data Analyst in Chennai, Tamil Nadu, India
Position: Bioinformatics Data Analyst Company: GenomicStar – A SaaS based Precision Medicine Platform Job Purpose: The Bioinformatics Data Analyst will play a critical role in the development, validation, and implementation of data analysis pipelines for various genetic test panels, incorporating state-of-the-art AI techniques. This role is integral to our commitment…
Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning [PeerJ]
Introduction The rapid proliferation of high-throughput sequencing in metagenomics, combined with the advancement of scalable computational tools, has allowed scientists to digitally isolate tens of thousands of microbial genomes from large collections of metagenomic datasets (Nayfach et al., 2021). Although these genomes are only the tip of the iceberg of…
The master growth regulator DELLA binding to histone H2A is essential for DELLA-mediated global transcription regulation
Peng, J. et al. ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400, 256–261 (1999). Article CAS PubMed Google Scholar Eshed, Y. & Lippman, Z. B. Revolutions in agriculture chart a course for targeted breeding of old and new crops. Science 366, eaax0025 (2019). Article CAS PubMed Google Scholar …
Sorting the Input Bam file by Read Id.
Sorting the Input Bam file by Read Id. 0 Hi All, I am trying to sort the deduplicated, filtered, sorted BAM file by read id to be used as an Input file for the Samblaster tool which identifies split and discordant read pairs from the bam file.I used samtools sort…
Paired-end reads reported without mates: how to play matchmaker?
Hi Everyone, I am currently looking at Acute Myeloid Leukemia (AML) paired-end WGS samples from the TARGET data ocg.cancer.gov/programs/target/target-methods#3241. A bioinformatician in our group remapped the samples from hg19 to hg38. Unfortunately, we do not have any copies of the hg19 version anymore. However, when I try to run anything…
Error in pipe output to samblaster from bwa-mem2
Error in pipe output to samblaster from bwa-mem2 0 Hi, I am trying to upgrade my command from bwa to bwa-mem2. This command usually works. bwa mem -M -R “@RGtID:idtSM:sampletLB:lib” human_g1k_v37.fasta sample.1.fq sample.2.fq | samblaster -M –excludeDups –addMateTags –maxSplitCount 2 –minNonOverlap 20 | samtools view -S -b – > sample.bam…
