Are any R package or methods available to simulate a label free bottom up proteomics expression dataset I have tried ’generate.ExpressionData’ function of ’imputeLCMD’ R package. It gives the normalized dataset. I have to test the normalization and imputation approaches on the simulated dataset....

   Dear Biostar Community, Currently I’m doing a phylogenetic study on samples. The samples were sequenced using MIG seq. The sequencing data is in fastq format. Using Julien Catchen’s Stacks, I was able to create a SNP matrix. From the SNP matrix, I was able to do a PCA and find that there are...

   Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of for each SNP awk ’BEGIN OFS t ; print ’ B.bed B .bed Next, I tried using bedtools window to find overlapping features between A.bed and B .bed, but couldn’t...

   Hi, I did a denovo transcriptome analysis of plant samples. and got the transcripts. I am new to RNA seq analysis, please guide me on how do I know that a particular transcript is a full length gene I need the full gene length complete coding sequence for functional validation of a particular...

   using bcftools Show us what you tried

   Hello everyone I have performed Kallisto; I understand the principle of pseudo alignment it works on. However, I cannot wrap my head around two things: . What exactly happens in indexing How does the indexed file look like I am unable to open my indexed file due to large size . I am using...

   Hello, I would greatly appreciate some help with this issue I’m having. Thank you in advance Summarizing the question in a post title was tricky, so I apologize if the title is unclear. I’ll explain in detail below. To start, I have two bed files, one with non overlapping regions of varying...

   Hi, guys, there is a question about the genomic gVCF file. I wonder that since gVCF contains the non var block records, why after merge all gVCF, there are still some NA in the merged gVCF file If I understand your question correctly, why do you still see no coverage no call areas even with...

   Hello, I have phased haplotype assemblies for human samples. The phased assemblies come in the form of haplotigs but I want to assign these haplotigs to chromosomes. After mapping haplotigs to chm with minimap , I have a bam file with aligned haplotigs. I want to create a fastq from this bam...

   Hi, guys, there is a question about the genomic gVCF file. I wonder that since gVCF contains the non var block records, why after merge all gVCF, there are still some NA in the merged gVCF file And in general, how many loci can be sequenced for each sample in WES Thank you for your time and...

   Thank you for replying here; this helped me figure out why MAPK was missing from my results. It was also marked as a pseudogene in the Ensembl v release. It’s unfortunate that the Cytoscape app can’t use old versions. I know it’s out of your hands for this version, but this may be useful...

   These are the first lines of the output: Please is it normal to have NA in the P value column CHR SNP BP A F A F U A CHISQ P OR : CNV GSTT B ...

   So I used the barcodes that I created combos of positions and and I obtained similar alignment stats as the paper I pulled the samples from. I’m thinking a lot of the barcodes in the reads were only off for a single base pair. STARSolo allows a single base pair in the read barcodes to...

   Thank you so much, it actually worked

   Hi efc e , First a caveat. the information we most need in order to help guide you to a successful conclusion is not provided in this post. We don’t know, for instance, if you have prioritized these variants, how you filtered them, what the criteria for doing so were if you did, and so forth....

   Hello, apologies if this has been asked before. But most answers tools I seem to find require some form of expression data to do pathway analysis. My situation is that I have set long read whole genome seuqenced samples and some normal tissue samples. I called and filtered variants from these....

   The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unless you anticipate having to compare to other samples on a shorter run, in which case, trim the fastqs to match the shortest reads you have

   I need to design a few synthetic RNA molecules with a known secondary structure ideally a single stem loop . I want to use them to test an RNA structure determination method, so it is important that I am confident about how the sequence is going to fold so that I can use the known structure to...

   HI I have a Delly output for an inversion event. The gene is on chromosome and it is on the negative strand. I’m trying to visualize how this will look as a transcript and I have a difficult time visualizing this. The output is POS , , STRAND POS , , STRAND ...

   Thank you, the csvtk spread is super useful. I usually import into R using lapply then Reduce using merge but this might be easier.

   Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.

   Open a new question, with details.

   I recommend https: bioconductor.org books . OSCA.basic normalization.html as well as the advanced section in this book.

   Hello everyone I am aiming to compare some single cell RNAseq datasets, specifically cell stress level between them. Considering cell type diversity in the tissue, I was thinking on experimental design as normalizing each dataset to housekeeping genes and then statistical comparison. The...

   thank you