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Biostars
28  mars     11h16
Comment: Nextflow ERROR : Timeout waiting for connection from pool
   As best as I can tell it is a combination of things. Did you try setting export NXF ENABLE VIRTUAL THREADS true in your shell You also need to upgrade to Java . nextflow has a slack channel where all their developers are active. You can join and post this problem there and or link to this...
    11h16
Flow Cytometry Data Analysis by Seurat
   Hello everyone. I’m now trying to analyze relatively big FACS data about samples, colors . I think Seurat is suitable for our purpose e.g. conducting dimensional reduction of the data such as tSNE , but does it make sense I have already analyzed FACS data using Flowjo manually...
    11h15
ONT direct RNA sequencing
   I have ONT direct RNA sequencing data consisting of fastq.gz files per sample. I need to merge all of these files into a single file. When attempting to combine them using the command zcat PAW .fastq.gz fld.fastq.gz, I encountered an error indicating that the files are not in gzip format....
    11h09
Comment: Coverage observed in introns in the Knockdown genes but not in knockout genes
   As per the image below obtained by Running RNASeQC the intronic reds aren’t that much See the knockdown samples enclosed in the Red box at least not more drastically different compared to other samples that underwent gene knockout. enter image description here : media images...
    11h00
Comment: Parsing fasta file by coordinates
   Am I understanding this correctly, that what you are looking for is any sequence where any part of the coord range overlaps with any other part of another coord range Even if that overlap were just one or two base positions
    10h54
struggle to get fasta files from ucsc goldenPath
   Hi all, I am very interested in get fasta seq mrna from a given genes IDs. My first approach has been to download from here https: hgdownload.soe.ucsc.edu goldenPath hg bigZips the refMrna.fa.gz file and then use bedtools getfasta rna to retrieve it: e.g: bedtools getfasta fi...
    10h44
Comment: convert cds to seurat object
   Did you check the data in the assay of the cell data set object
    10h42
Comment: calculate mismatch rate from VCF file
   use the output of samtools mpileup
    10h18
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
   It’s log pvalue, you miss the minus. Some people use indeed pvalue, but since you’re filtering on padj, I would show log padj rather than pvalue. It’s better to interpret in terms of common cutoffs.
    10h13
Volcano Plot Output Inquiry: Graphs Facing Down
   volcano plot results from rstudio Hello Biostar community, I’ve been encountering an unusual output in my volcano plots, and I’m seeking some insights from the community. Typically, all my graphs tend to come out facing downwards. I’ve used the following codes for analysis: r Change...
    09h52
Comment: calculate mismatch rate from VCF file
   Thank you for your reply My bad. I didn’t mention that I want to get the mismatch rate for each site. Is this error rate for each site
    09h52
Answer: Interproscan taking so much time
   Parallelize. Chunk your transcriptome into groups of something like or less if you want it to go faster , and run an array across your different input files at the same time. This type of processing will help in a lot of different bioinformatic analyses.
    09h49
Comment: Nanopore data filtering using fastp
   Ah, sorry, I was thinking of the wrong command. You can either use seqtk sample or seqkit sample . I would recommend the former if your files are particularly large.
    09h44
Comment: Variant calling of GBS data
   It does not output warning when I skip flags for MQRankSum and ReadPosRankSum java jar Xmx G gatk.jar VariantFiltration R reference.fa V A raw snps.vcf O A filtered snps.vcf filter name QD filter filter QD . filter name FS filter filter FS . filter name SOR filter ...
    09h43
Comment: Merging featureCounts output for different species
   Is there any list of homology you could use for this merging Maybe this would be helpful
    09h40
Comment: Variant calling of GBS data
   again, remove the spaces SOR . SOR
    09h39
Comment: Variant calling of GBS data
   It is still giving same warning java jar Xmx G gatk.jar VariantFiltration R reference.fa V A raw snps.vcf O A filtered snps.vcf filter name QD filter filter QD . filter name FS filter filter FS . filter name SOR filter filter SOR . filter name MQRankSum...
    09h37
Merging featureCounts output for different species
   Hi I have bulk RNAseq data for different species for which I created separate count.txt files using their respective annotations.gtf files. I then removed all the unnecessary info them to get a simple count matrix as shown below. What I want to do now is merge these count files into one...
    09h28
Interproscan taking so much time
   I’m new to transcriptomic data analysis and currently in the process of running InterProScan version . . on my transcriptome, which consists of approximately , contigs with an N of, and L of , . I’m utilizing the IFB cluster, allocating CPUs and GB of RAM for this...
    09h26
Comment: Nextflow ERROR : Timeout waiting for connection from pool
   It doesn’t make sense how to change the threads and in my case it is not working What kind of problem is that is it related to Amazon to the memory of my computer, to a number of threads, or to the internet connection It is completely strange to me and I cant figure out how to solve it
    09h22
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
   I have a FASTA file like this: seqA AAAAAAAAAA seqB AAAAAAAAAA seqC TTTTTTTTTT seqD CCCCCCCCCC seqE CCCCCCCCCC seqF AAAAAAAAAA I’m recently learning SeqKit, and I’ve found that rename can append N in the header based on...
    09h21
Comment: STAR aligner options
   I have finally found out the reason behind this behavior. As pointed out by dsull , the beginning of the alignment of read to the rattus genome is soft clipped. My Rattus genome is assembly version . downloaded from Ensembl , with annotations from Ensembl release . When looking at TAC ...
    09h19
Comment: Variant calling of GBS data
   Right Pierre, thanks.
    09h18
Comment: Variant calling of GBS data
   remove spaces in expressions. ’MQRankSum
    09h16
Comment: Variant calling of GBS data
   enter image description here : media images f e af a d b