atpoint All I need is the mitochondrial cutoff used in the brain. I have no idea how to decide that. I hoped someone here has knowledge in this domain and could help.

   Hey everyone, I see in multiple articles, people have not used beagle for phasing but after filtering they directly go to ldhat analysis i am assuming that converted the files in phased format using ldhat vcftools option . Phasing using beagle isn’t necessary right Thanks, Chandan

   You can use efetch to query for metadata from SRA but you can’t use efetch to download sequence data. for example you can do this: efetch db sra id SRR format runinfo Run,ReleaseDate,LoadDate,spots,bases,spots with mates,avgLength,size MB,AssemblyName,download path...

   not directly via efetch but do have a look at https: sra explorer.info , great tool to get the necessary cmdlines to download data sets : https: sra explorer.info

   you can use sratool kit that works.

   Before I ask my question I would like to say that I am new to RNAseq data. I have been downloading raw data from the NCBI databases using the efetch i.e. Entrez . Is it possible to download raw sequence reads from the SRA database using the same method also using Bio.Entrez in Biopython or do...

   Again, it’s pretty arbitrary, but a gene found in only cells is unlikely to be informative if you don’t have some ultra rare population of interest or something. Pick a conservative threshold and move on, this isn’t going to make or break your analysis.

   A : :HWTVNDSX : : : : That fastq header format was used by Illumina for data at least a decade or so ago, prior to release of CASAVA v. . , when it changed to current format we are familiar with . indicated data from R read. Oddly SRR being referred to is a...

   Your SAM output is indeed incorrect: SRR . chr ...cut... XS:i: A : :HWTVNDSX : : : : You can see it mysteriously ends on a read name, so this is invalid aux tag format. The bwa mem man page has this to say about the C option: C ...

   Hi, I’m facing the same issue with VQSR vs hard filtering. I have similar plots. Did you come across any helpful answers or conclusions on this Would love to hear your thoughts

   Looks like your download was not complete. You will have to try again. I see that folder in the source after download.

   Hello, I am trying to run the PICRUSt pipeline, but I encountered an issue where the pro ref folder is missing from the cloned repository. I have checked the default location default files proka

   You can use color coding as described in: https: groups.google.com g igv help c gUvYp imn U https: groups.google.com g igv help c IyBzO j E ItemRGB is described in BED format spec: https: genome.ucsc.edu FAQ FAQformat format

   Hello everyone, I am currently working with a .bed file containing genomic regions associated with different features: DMR Differentially Methylated Regions , LMR Low Methylated Regions , UMR Unmethylated Regions , and histone mark peaks. To simplify my analysis, I merged these different .bed...

   Please don’t ask the same question twice, it was answered by multiple people before: https: www.biostars.org p Note: The data at hand is composed of neurons and glial cells. Should the thresholds change for each cell type Maybe yes, I often put celltyper specific thresholds....

   Thank you for the answer and detailed explanation. This is really helpful as now I’m getting the general idea of how this kind of analysis works which in turn makes me able to judge whether this is what I am potentially interested in comparing. Oh and as for the second part in that case I’m...

   This is definitely one way to do this analysis. You need to be slightly careful about interpreting the results though. Under the reduced model X Y , if the LFC for a gene is when treated with X, and when treated with Y, then the expectation is that the LFC of a sample treated with both...

   I have obtained normal brain snRNA seq data, but due to my limited experience and knowledge in this tissue, I need guidance on applying pre processing steps. Firstly, what is the usual threshold for filtering out mitochondrial genes based on their percentage of total counts In one brain tumor...

   Hello, For a while now my variant calling workflow SNVs and InDels has filtered mapped reads from BWA to remove discordantly mapped reads, i.e. keeping only properly paired reads, and remove secondary alignments. samtools view f F Obviously for identifying structural variants...

   nevermind, just follow what https: www.biostars.org u says after all those years I should know not to contradict Pierre : I just realised that he’s doing the opposite as what I thought of doing, it replaces all the uppercase letters,leaving the lowercases and then you can, following the...

   Hi, I know it is common that we should use TPM or FPKM normalized mixture matrix as input for CIBERSORTx, but I don’t see any statement about specific format of values in the mixture matrix from the tutorial of CIBERSORTx, so I wonder whether we could use count matrix as the input of mixture matrix...

   Yeah it would probably be the sum.

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   I have Illumina Human Methylation platform to analyze. I have R version . . , packageVersion sesame . . ’ packageVersion sesameData . . ’ packageVersion ExperimentHub . . ’ I am trying to perform sesameDataCacheAll for methylation data....

   In my case, I have a dataset that is the result of data integration of different datasets where cells have been previously filtered in terms of nfeatures, ncounts and percentage of mithocondrial DNA individually different values of these parameters have been used in each dataset . The final...