You can, if you use RStudio via Docker, for example bioconductor bioconductor docker . I currently manage many different projects with this strategy, with different R and Bioconductor versions independent of any permanent host machine. Oldest project goes back to R . . and Bioc . . Together...

   Pierre Lindenbaum I see. So, I can actually manipulate just one single RG tag at the time with samtools Which flag should I use, or should I just get the header from the BAM file add the tag and set it as the new header Let me know, thanks

   RG tag L is missing the the BAM header. You should have something like this in the BAM header RG ID:L SM:L may be you can add this with sam reheader

   Hi there I recently start working with some archaic samples aDNA , specifically two high coverage samples of Neanderthal and Denisova. The latter has on single BAM file aligned to GRCh and already sorted; unfortunately, Neanderthal has five BAMs which were not sorted and needed to be merged... ...

   Is there any way to find through sam or bam file that which chromosomal position are maximum reads aligning to samtools depth in.bam awk F ’ t’ ’BEGIN BEST DEPTH ;BEST ; DEPTH int ;if BEST DEPTH

   Hello Franco. I am very much new with bioinformatics but I have been tasked with studying the radius of gyration of a timeseries of a protein contained in a pdb file. I managed to learn to use biopython and parse the pdb file into all the successive models but I am struggling to understand how I...

   That makes a lot more sense. Thank you.

   Hi all, I am analysing NGS amplicon reads of crisper gene samples. I do not know exactly which genes do they belong to because if I align reads against gene sequence that was supposed to be using BWA it gives identity however by aligning reference genome I get alignment rate. Now how...

   Type help read.idat and read the example at the bottom of the page, which shows you how to set the other Detection component of the EListRaw object. Alternatively, you could just type example read.idat . Questions so that are so specific to limma are best sent to the Bioconductor...

   Accurately assessing a few QC metrics is trivially easy. Assessing the significance of variants in a clinically responsible way is really, really hard.

   If and really are the same library, you should rename the fastqs, or make symlinks, such that they have the same sample name, but different lanes. Cellranger will naturally take them all in together.

   Just delete the index read files. They just take up space and will never be used.

   Yes. Why wouldn’t you use, say, AddOrReplaceReadsGroups

   Hi there I need suggestions and guidance. I am working on a meta transcriptome project focusing on environmental samples, primarily bacteria. The Trinity assembler was used to obtain the assembly. I filtered a list of transcripts for primer design, but most of the transcripts do not start with...

   Thank you. Decreased the threads to changed the threads: in the config file; but it was somehow using . It did run for sometime but the following error came : home akk software library CIRIquant env akk kashyap: circ analysis new analysis CIRIquant config home akk circ analysis new...

   See this section on how to use tximport to import StringTie output for DESeq processing: https: bioconductor.org packages devel bioc vignettes tximport inst doc tximport.html StringTie

   Can you explain the normalization or give me a link that describes it, please Comparison across samples will always be caveated as RNA seq yields relative measures.

   Sorry, I see how harsh I come across. It’s not good practice to use multiple versions of R in the same project. I can understand legacy project dependencies and why fix something that isn’t broken scenarios, but designing around these dependencies is asking for unmanageable headaches down the line.

   I used the stringtie e B command and received a file like the one attached to this post enter image description here When using it in R, I received an output saying that I needed a .ctab file. I tried using the cufflinks environment with the tablemaker command but it said that there was...

   I have ensured that I am using the latest version of MEGA and that other applications are not consuming excessive resources during the analysis. I have also checked that there is sufficient disk space available. You have answered your own question, probably without realizing. If any kind of...

   Dear MEGA Community, I am encountering an issue with the MEGA software during phylogenetic analysis on my powerful computer. Despite having GB of RAM, an Intel Core i H processor, and a GeForce RTX graphics card, the analysis stops working after about hour and minutes and does...

   I am analyzing a microarray data set generated with Illumina HumanHT v . I have files with the idat extension and use the read.idat function in limma to read the raw microarray data into an EListRaw. I am trying to remove probes with very low expression and don’t see a straight path to doing it...

   Some of us are still learning and fall foul to knowledge limitation fairly regularly. Luckily we have people to put us in our place.

   I know that I should be able to collect protein sequences from the blastp results into a file, but I do not know how to do this. You can do that by extracting the sequences you need from the custom database using blastdbcmd utility included in blast . See help: https: www.ncbi.nlm.nih.gov...

   I got the normalized gene count from gtex portal. they use inverse quantile normalization