elkonlab / scapa Goto Github PK

I wanted to generate a Cluster annotation file that includes the barcode and another one cluster column, so how can I add a clustered column in the barcode tsv file?

Dear authors,
Can you show me your example codes to generate the peak graph in figure 1C or 2C using the scAPA output files? Thanks in advance!

very nice work! But I have some questions about this pipeline:
1.hg38 is ok? Or It just depends on which one you used when you made alignment by cellranger pipeline?
2. what is the format about "chromosome length file" in the "configfile.txt" file? It is a .fai file? Can you give a demo?

I got an error "could not find function write_log_start" after runing the scAPA.shell.script.R. I didn't find this function in script, and found that "write_log" were also not in the script. Is the script incomplete or these function were in some R packages i not found?

Hello, Thank you for your developing for this tools.

But here I cannot understand the logic behind. You set this judge sentence.

if (!all(file.exists(paste0("./temp/UB.", samples.vector, ".bam.bai")))) { write_log(stage = "samtools index", success = F) stop("samtools index did not end, shell script did NOT end!") }

I do not know why should I always run two times then it can detect the .bam.bai file ? Thanks you

Hi! I wonder how much RAM this whole process requires, for a bam file of 14G?

hello, does the PAi in the results represent the location information, including pAi.cells and pAi.clus

May I ask if you can provide detailed explanations of files such as hg19. introns.rda, hg19. utr. rda, so that I can replace them with GRCh38; Thank you very much.
Or the reference genome will not have a significant impact? ( I used hg38 for cellranger processing. )

Hi and thanks for the very interesting pipeline! I have a question about the scAPA output files.

I've run scAPA.shell.script with the provided downsampled BAM files of Lukassen et al.. The -sc option was false, otherwise the default settings were used. The run finished without errors and produced the expected output files.

The contents of the file summary.Introns.txt are:

Number of peaks passed fillter: 10512
Number of significant (FDR < 5%) APA events: 1645

The contents of the file summary.UTR.txt are:

Number of peaks passed fillter: 5847
Number of significant (FDR < 5%) APA events: 286

However, the file APA.events.txt is empty, and the file Intronic.APA.events.txt contains the text:

x
p-value
q-value

Shouldn't the events files contain descriptions of the identified, significant APA events?

-Darius

Hello,
it's a really impressive method. And I want to use this method in my project. But I have multical 10X single cell samples, and I ran one by one following your 'Instructions for Manual Implementation of Our Pipeline'. I got multical Peaks.rds files but I was stucked in merging them. Could you show me how could I merge mutical samples' peaks.rds files or merge multical objects in R and how to extract only some cells I was interested in the 'peak' object.
Thanks and Merry Christmas!

Your tool is fanstastic and I'm super interested in looking this APA patterns in my data, I work with Drosophila I was wondering how can I implement this using Drosophila?

thanks

Hi,

Does scAPA really require the release 2.2.0 of Drop-seq tools or can I use the 2.3.0 version?

Best regards,
Daniel