squid

squid copied to clipboard

Aborted core dumped error

2

Hello, I ran Squid v1.5 using 12 cpus and 96 GB RAM with the following command: `squid -b AUR1.Aligned.sortedByCoord.out.bam -c AUR1_chimeric_sorted.bam -o AUR1.squid.fusions` Here is the output and it was...

pcantalupo

Hi, I am running squid with two types of inputs: 1) Samples aligned with STAR 2) Samples aligned with BWA When using STAR output, I get less than 100 SV...

yasin-uzun

Hi, I am trying to use Squid for calling SVs in my datasets. I have 87 samples and all are processed in the same way. I ran Squid as follows:...

yasin-uzun

Hello! I get this error while running Squid. The chimeric sam file generated through STAR run is empty and it fails when run as a bam file with Squid. Please...

think-o

--chimOutType SeparateSAMold will be deprecated from STAR. Would it be possible to migrate to a single bam file feed as in bwa to make squid future-proof?

rannick

I have been having this issue while running SQUID to obtain transcriptomic structural variants from RNASEQ data. This is the error that I have been receiving. ```bash [Thu Aug 12...

tamal1307

Hello! I was wondering if there is an option for the number of threads that can be used by Squid

think-o

Hello. I have a scRNA-seq seurat object gene expression matrix (rows: genes, columns: cells). May I ask if I can use squid tool for scRNA-seq data? If yes, what would...

levinhein

Hi, Can squid call SV for long reads RNA-seq (cDNA) data from Oxford Nanopore or Pacbio now? Thank you very much! Best, ping

sunshine-lp0

Linker error when compiling SQUID

3

Here is the error message when I run make on the Makefile of squid `src/ReadRec.o: In function `BuildChimericSBamRecord(std::vector&, std::vector const&, std::__cxx11::basic_string)': ReadRec.cpp:(.text+0x34f9): undefined reference to `BamTools::BamAlignment::BamAlignment(BamTools::BamAlignment const&)' src/SegmentGraph.o: In function...

Lyn16