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Hello,
Sorry to bother you again.
I'm attempting to run Novel-X on the following 10x Genomics bam file : ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/10XGenomics…
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When multiple interleaved libraries are used which are stored in a different location but with the same name, the file split procedure overwrites the previous split files.
My use-case: I gave two 10…
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Thanks!
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Hello,
I tried to run scaff_reads on my 10X raw data with:
`scaff_data reads.dat reads_1.fastq reads_2.fastq > try.out`
Where, my reads.dat file had:
q1 = /10X_RAWDATA/S1_L008_R1_001.fastq.gz
q2=…
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I'm working to identify SVs in 10X linked-read data using methods alternative to longranger. What is the best way to call SVs from the adjacency info given in the bedpe file, or is there a tool that d…
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### Description of the bug
Hi there!
I'm currently using the pipeline to assembly some data, and I find myself having issues with the polishing step. According to the error message, the longranger…
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Hi,
Could you tell me how I can use the linked-reads such as chromium and Hi-c reads?
Is it possible use the bam files from them to replace the long reads?
I tried to find how to use them in th…
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Ideally this would be an optional input to markduplicates_helper.sh. Default behavior would be undefined. For UMI data, the tag is used to mark duplicates within a single molecule family.
Example: BA…
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Hello,
I am running LinkedSV on a 10x linked-read WGS dataset of a highly rearranged human cell line. The alignment was done previously with the 10x Longranger pipeline. LinkedSV ran through, the r…
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Hi.
I'm using 10x linked-read pipeline and acquired bam files through LongRanger tool.
I'm trying to apply Manta 1.6.0 for these bam files, but the error has occured. I looked upon similar arti…