STARsolo: Cell barcode in BAM file is from previous read. #593
Comments
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Hi Gert, I fixed the problem with shifted CR/CY/UR/UQ output, please try it from GitHub master. Cheers |
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Thanks a lot for the fix. Some minor "issue", when Another thing I noticed before. If your input barcode file contains duplicate barcodes, //load the CB whitlist and create unordered_map
ifstream & cbWlStream = ifstrOpen(soloCBwhitelist, ERROR_OUT, "SOLUTION: check the path and permissions of the CB whitelist file: " + soloCBwhitelist, *pP);
string seq1;
while (cbWlStream >> seq1) {
if (seq1.size() != cbL) {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR in input CB whitelist file: "<< soloCBwhitelist <<" the total length of barcode sequence is " << seq1.size() << " not equal to expected " <<bL <<"\n" ;
errOut << "SOLUTION: make sure that the barcode read is the second in --readFilesIn and check that is has the correct formatting\n";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_INPUT_FILES, *pP);
};
uint32 cb1;
//convert to 2-bit format
if (convertNuclStrToInt32(seq1,cb1)) {
//cbWL.insert(cb1);
cbWL.push_back(cb1);
} else {
pP->inOut->logMain << "WARNING: CB whitelist sequence contains non-ACGT and is ignored: " << seq1 <<endl;
};
};
//int comp1 = [] (const void *a, const void *b) {uint32 aa=*(uint32*) a; uint32 bb=*(uint32*) b; if (a
qsort(cbWL.data(),cbWL.size(),sizeof(uint32),funCompareNumbers<uint32>);
According to https://stackoverflow.com/questions/12308243/trying-to-use-qsort-with-vector qsort is also slower than std:sort Wouldn't it be better to use a |
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Hi Gert, Thanks for the thorough tests and very helpful reporting!
Cheers |
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Hi Gert, I have a made a new release that's supposed the fix the problem CR/CY... tags and Unmapped problems. Thanks for reporting them! |
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Hi Alex, Thanks for fixing those issues. |
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Hi Gert, my plan is to Cheers |
Read with barcodes:
Read with RNA.
BAM file mapped with STAR solo has the wrong barcode (
CR). The barcode it seems to put there is the barcode of the previous read in the input fastq file.BAM file mapped with CellRanger does not have that problem:
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