You’re right They look identical before and after purging. And, as GenoMax mentioned, since the number of chromosomes is closer to 18, then I’d say that you should keep the purged assembly (which hasn’t lost anything important in terms of BUSCOs and k-mer completeness). It’s just weird that the...

   Hopefully you have your answer by now, but in case not: The NHGRI-EBI GWAS Catalog is by far the biggest resource of human GWAS summary statistics. Several of the other resources you might find, such as the IEU Open GWAS Catalog, the Knowledge Portal Network (https: kp4cd.org ), and GWAS Central,...

   Title should say software infrastructure focus since plain infrastructure would generally be hardware related :-)

   Hi Madelaine. Do you know if they sponsor a Visa for international applicants?

   The Stowers Institute has an opening for a [Bioinformatics Specialist][1] to assist the Computational Biology core facility with biological data processing and analysis. The Bioinformatics Specialist will use computational tools to process, transform, visualize, and analyze datasets primarily...

   I made a special program that automatically finds the optimal value of -l of Hifiasm (https: github.com shelkmike Mabs).

   I would like some clarification on how to correctly intersect RNA modifications with transcript features. I have a bed file with extracted modifications from modkit. I would like to intersect these modifications with transcript feature beds like cds.bed, 3utr. bed (extracted from gtf file). How do...

   Hello everyone, We are excited to introduce FastDup, a new high-performance tool for marking duplicate reads in NGS data, recently published in Bioinformatics. Duplicate marking is a critical step in variant calling pipelines (e.g., GATK Best Practices), but standard tools like Picard...

   Hi. I am looking for paper or justification about using : sign(log2Fold ) -log10(pvalue) Do you have any ? Thanks

   Hi panos I ran Hifiasm with mostly the default options hifiasm -o asmOUT sample hifiasm -t 48 --n-hap 1 --telo-m TTAGGG PB01.fastq I see on Hifiasm github the details for -l option you mentioned and it says Level of purge-dup. 0 to disable purge-dup, 1 to only purge contained haplotigs, 2 to purge...

   typically 11 are core and some accessory ( in reference they are 4 but some strains can have more or less than 4) and during comperative analysis with reference (after purge dups) the remaining do align exactly to the known core and accessory chromosomes. so i was kind of really happy that i got...

   In the hifiasm github, they specifically mention that Hifiasm does automatic purging of the duplicated haplotigs. What you might want to do instead, is make the built-in PurgeDups algorithm more aggressive by changing the -l parameter. I haven’t tried it though, so I don’t know what the result will...

   How many chromosomes do you expect for this organism? Is 18 is more or less in-line than 122?

   HI, I have this nieve question which is causing some confusion. Is it a good idea to run Purge dups on PacBIo Hifi reads based assemblies generated with Hifiasm. In hifiasm assmebly log file i see some tags like [M::purge dups] and a quick Chat-Gpt search suggested that i don’t need to run it...

   Hi all, I have a dataset from a base editing experiment where some spacers show efficient editing, while others show little or no editing. In addition, among the edited sites, some show the intended conversion (e.g. A to G), whereas others show unintended or mis-editing events (e.g. A to C or A to...

   There is gene- and transcript level. Gene level means that your counts are for genes not transcripts. Methods like STAR featureCounts give gene level counts right away. Then there are the trascript quantifiers, such as salmon, kallisto, stringtie, etc, that give transcript abundances. This can be...

   Hello, I am trying to download and prepare RNA-seq data from the TCGA-LAML project using the TCGAbiolinks package in R. The GDCquery and GDCdownload steps work, but GDCprepare fails with an error about a missing disease response column. The code I ran: library(TCGAbiolinks) query <- GDCquery...

   Hello is there any one who know’s how we can find out the common consensus motif region from a list of HOMER identfied sequences and MEME analysis.. Thank You

   edgeR’s catchSalmon function automatically reads the aux info files on the fly. You do not need to parse these files yourself. You just give catchSalmon the name of the directory containing the Salmon output, and it does the rest. However, if you are working with a poorly annotated organism, and...

   Ah, so improving on the transcript level will not also improve on gene level. I guess that would make sense since all of the reads would just go to the gene - it wouldn’t matter at all how they are subdivided among transcripts. My transcripts were reconstructed using stringtie, so I wouldn’t place...

   Yes; this is the expected behavior. The Gibbs samples for salmon are stored in a binary format.

   Reddit r cellculture and r labrats is the go-to. StackExchange is quite mess these days.

   This forum is focused on bioinformatics issues so this question is off-topic for this forum. While someone may answer, please post this question over in an experimental biology forum, biology stackexchange or relevant reddit.

   Hello everyone, I am working on establishing primary cultures from human lung cancer tissue samples (patient-derived cells, PDCs). A common challenge I face is the mixed outgrowth of both epithelial (presumably tumor) cells and fibroblasts in the same flask. I have tried differential trypsinization...

   and I read that using Gibbs sampling improves EdgeR’s ability to correction for dispersion ...on transcript level, are you aware of that? Not on gene level, and 99% of DE analysis are done on gene level, so not resolved by transcripts per gene. Do you really want and need transcript level, as it is...