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Hello
I downloaded and installed TRUST4 on Linux using git clone
However when I start the run with this command on top of the image
The run start but I get the following error, cant resolve it:…
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Here is my code and the bug:
$ ./run-trust4 -b all_contig.bam -f all_contig.fasta -o TRUST_all_contig_toassemble --ref mm39.fa --barcode CB -t 4
[Tue Mar 12 11:32:23 2024] TRUST4 begins.
[Tue M…
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Hello,
I have a question about the filtering steps are done by TRUST4? I read the paper, but wanted to know if there are more criteria for filtering the reads/cells, which are not shared in the pap…
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Hi, firstly thank you for creating the nabseq_nf pipeline.
I've been running the nabseq pipeline on Seqera/Tower and noticed that the biggest bottleneck is the `subset_aligned_reads ` step, which f…
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Firstly thanks for the great tool! When I ran TRUST4 on bam file of 10x scRNA-seq, some errors happened in only part of samples. And Rerun did not solve the error. I installed TRUST4 form github. This…
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Hi
I need your personal point of view please
I have two `bulk RNA-seq` patients (PBMC) on which I run `mixcr`
For the same two patients I have `5' single cell` on which I run `TRUST4`
I a…
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When running with the command:
`./TRUST4/run-trust4 --od ./trust4 -o run1 -f refs/hg38_bcrtcr.fa --ref refs/human_IMGT+C.fa -u data/*_R2_*.fastq.gz --barcode data/*_R1_*.fastq.gz --barcodeRange 0 1…
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These thoughts are based on our discussions around #409 and other single-cell stuff. However, as they are rather generic in nature I created a new ticket. As I assume that issues like these will come …
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I attempted to analyze BCR sequencing data generated using the GEXSCOPE® Single-Cell Immune Receptor Library Construction Kit with the multi_vdj_full_len tool. However, I encountered an error during t…
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Hi,
First of all, tremendous thanks for developing this wonderful tool. I have tried this tool with scRNA data recently and have dug into the previous issues, and I have summarized some questions b…