Tag: XS

Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma | BMC Medical Genomics

Sia D, Tovar V, Moeini A, Llovet JM. Intrahepatic cholangiocarcinoma: pathogenesis and rationale for molecular therapies. Oncogene. 2013;32(41):4861–70. CAS  Article  Google Scholar  Sungwan P, Lert-Itthiporn W, Silsirivanit A, Klinhom-On N, Okada S, Wongkham S, Seubwai W. Bioinformatics analysis identified CDC20 as a potential drug target for cholangiocarcinoma. PeerJ. 2021;9:e11067. Article …

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AURKA is a prognostic potential therapeutic target in skin cutaneous melanoma modulating the tumor microenvironment, apoptosis, and hypoxia

Aran D, Hu Z, Butte AJ (2017) xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol 18(1):220. doi.org/10.1186/s13059-017-1349-1 CAS  Article  PubMed  PubMed Central  Google Scholar  Bajor DL, Mick R, Riese MJ, Huang AC, Sullivan B, Richman LP, Torigian DA, George SM, Stelekati E, Chen F, Melenhorst JJ, Lacey SF,…

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MBEDTLS 2.27.0 and stack – githubhot

Since MBEDTLS 2.27.0 is merged, a call to mbedtls_x509_crt_verify() fails: E/TC:? 0 E/TC:? 0 User mode data-abort at address 0x10ff3c (write permission fault) E/TC:? 0 fsr 0x0000080f ttbr0 0x24067859 ttbr1 0x24060059 cidr 0x2 E/TC:? 0 cpu #0 cpsr 0x60000130 E/TC:? 0 r0 0x0010ff38 r4 0x0010fb38 r8 0x00110380 r12 0xfffd34b4 E/TC:?…

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r – ggplot2 and grid.arrange, place legend below arranged plots

I am facing a problem when I arrange 2 ggplots next to each other using grid.arrange(). I want to place a legend evenly below both plots. So I have (pseudocode): p1 <- ggplot(data = df, aes(group = name, color=as.factor(fac), y = ys, x= (xs))) + geom_point() + geom_line() + theme(legend.position=”bottom”)…

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Frontiers | Association of Maternal Dietary Habits and MTHFD1 Gene Polymorphisms With Ventricular Septal Defects in Offspring: A Case-Control Study

Introduction Congenital heart disease (CHD) refers to a group of anatomic heart and great vessel malformations that arise during the embryologic development of the fetus. CHD is one of the most prevalent birth defects, affecting around 2.50 out of every 1,000 births in China (1), and it imposes a substantial…

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bwa , 2 files fastq to 1 sam

bwa , 2 files fastq to 1 sam 1 i have this problem, please, help me, I’m trying it too from Mac OS Catalina I am creating a sam file, with 2 fastq files, using bwa I apply the following command bwa mem -t 2 GRCh38.primary_assembly.genome.fa.gz V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz V350019555_L03_B5GHUMqcnrRAABA-556_2.fq.gz > V350019555_L03_B5GHUMqcnrRAABA-556.sam…

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[Bug 1951032] Autopkgtest regression report (glibc/2.31-0ubuntu9.4)

All autopkgtests for the newly accepted glibc (2.31-0ubuntu9.4) for focal have finished running. The following regressions have been reported in tests triggered by the package: snapd-glib/1.58-0ubuntu0.20.04.0 (armhf) apt/2.0.6 (armhf) libmath-mpfr-perl/4.13-1 (armhf) art-nextgen-simulation-tools/20160605+dfsg-4 (armhf) ruby-nokogiri/1.10.7+dfsg1-2build1 (armhf) r-cran-rgdal/1.4-8-1build2 (armhf) arrayfire/3.3.2+dfsg1-4ubuntu4 (armhf) libpango-perl/1.227-3build1 (armhf) libimage-sane-perl/5-1 (s390x) ruby-bootsnap/1.4.6-1 (arm64) mle/1.4.3-1 (ppc64el, arm64) libsyntax-keyword-try-perl/0.11-1build1 (armhf)…

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Sp.stats and PyMC3 logps different – Questions

Hi everyone, I am fitting a geometric distribution to the following data: [40000, 600, 1500, 30000, 12000, 25000, 65000, 1500, 40000, 10000000, 25000, 2000, 2000, 500, 800, 1500, 30000, 850, 25000, 1000, 15000, 40000, 9000, 3000, 12000, 1000, 1000, 1500, 10000, 25000, 7000, 35000, 30000, 25000, 750, 20000, 7000, 1500,…

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Issue with installing QIIME2 2021.11 on Windows 10 – Technical Support

Hi QIIME support team, I’m attempting to install QIIME2 on my Windows 10 machine. I installed Anaconda3, then set up conda to run in Git Bash: echo “. ${PWD}/conda.sh” >> ~/.bashrc Once I restarted Git Bash and activated Conda, I installed python-wget because installation of wget kept getting the following…

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Exec format error in unmapped bam file

Exec format error in unmapped bam file 0 Hello I created unmapped bam file from fastq file (sample 1). When I tried to search the bam file using query name, I got the ‘Exec format error’ #1_ucheck.bam: unmapped bam file from Sample 1 fastq file code: samtools view 1_ucheck.bam |…

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MAPQ (Mapping quality) of 0 for most reads from BWA-MEM2 (with no secondary alignment or other apparent reason)

Hello, I got a very weird output from BWA-mem2 – most of the reads have mapping quality of 0, even though there is no secondary alignment or anything else suspicious. I got sequencing data that was aligned with Novoalign to hg18, the data was bam files. I needed to realign…

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Does Hisat2 automatically align strandedness

Does Hisat2 automatically align strandedness 0 I’ve been using Hisat2 to align some RNA. RNA was prepped using NEB Directional library kit. When I originally aligned, I did not use the –rna-strandedness option. I then realised I do want stranded, as part of my reference (which is human genome plus…

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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…

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Bwa sampe error 999

Bwa sampe error 999 25-08-2021 I’m getting the following error message when I try to import into 1aa.vremenagoda54.ru file (using samtools import). [samopen] SAM header I’m using bwa aln to find coordinates and bwa sampe to…

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No cell barcode information in BAM files.

No cell barcode information in BAM files. 0 My BAM file seems to be missing information on cell barcodes. I find that each BAM file represents the sequencing result of a cell. Here’s what I found when I combined dozens of BAM files. Can someone tell me how to find…

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Mapping quality and XS score

Mapping quality and XS score 0 Hi, I am currently looking through bam files using igv to manually check if the mutations not called by Mutect2 are really an error or not. Until now, to filter reads with low quality, I have used only MAPQ > 30 and didn’t consider…

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How to convert mapping bam file to fastq without loseing the mapping information

How to convert mapping bam file to fastq without loseing the mapping information 0 Hi all, I want to create my RNA mapping data into a library for further analysis. Now I have bowtie2 mapping data, which is in bam files, I now use bedtools to extract fastq mapping reads…

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