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alexdobin / STAR

RNA-seq aligner
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mix of single and paired reads using --readFilesManifest #1698

Open schnabelr opened 2 years ago

schnabelr commented 2 years ago

Hi Alex, star-2.7.9a It appears that --readFilesManifest does not like a mix of single and paired reads. If I run using a manifest of all of one type it works fine. Below is what my manifest looks like that does not work. Is this by design that it only takes one read type? If so, is it possible to make this work for a manifest of intermixed paired and unpaired reads?

The use case is for data that comes out of read trimming (trimmomatic in this case) where one read was removed due to quality etc. and three files are written for each input paired set of files (Paired, F only, R only). I believe it would be beneficial to have all of these run together since I'm doing --twopassMode Basic, am I mistaken?

Thanks Bob

AN.73651.45446.R.AP.01.1.P.fq   AN.73651.45446.R.AP.01.2.P.fq   ID:AN.73651.45446.R.AP.01       SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.01.1.U.fq   -       ID:AN.73651.45446.R.AP.01UF     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.01.2.U.fq   -       ID:AN.73651.45446.R.AP.01UR     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.02.1.P.fq   AN.73651.45446.R.AP.02.2.P.fq   ID:AN.73651.45446.R.AP.02       SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.02.1.U.fq   -       ID:AN.73651.45446.R.AP.02UF     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.02.2.U.fq   -       ID:AN.73651.45446.R.AP.02UR     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.03.1.P.fq   AN.73651.45446.R.AP.03.2.P.fq   ID:AN.73651.45446.R.AP.03       SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.03.1.U.fq   -       ID:AN.73651.45446.R.AP.03UF     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.03.2.U.fq   -       ID:AN.73651.45446.R.AP.03UR     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.04.1.P.fq   AN.73651.45446.R.AP.04.2.P.fq   ID:AN.73651.45446.R.AP.04       SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.04.1.U.fq   -       ID:AN.73651.45446.R.AP.04UF     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.04.2.U.fq   -       ID:AN.73651.45446.R.AP.04UR     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.05.1.P.fq   AN.73651.45446.R.AP.05.2.P.fq   ID:AN.73651.45446.R.AP.05       SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.05.1.U.fq   -       ID:AN.73651.45446.R.AP.05UF     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.05.2.U.fq   -       ID:AN.73651.45446.R.AP.05UR     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.06.1.P.fq   AN.73651.45446.R.AP.06.2.P.fq   ID:AN.73651.45446.R.AP.06       SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.06.1.U.fq   -       ID:AN.73651.45446.R.AP.06UF     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.06.2.U.fq   -       ID:AN.73651.45446.R.AP.06UR     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.07.1.P.fq   AN.73651.45446.R.AP.07.2.P.fq   ID:AN.73651.45446.R.AP.07       SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.07.1.U.fq   -       ID:AN.73651.45446.R.AP.07UF     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.07.2.U.fq   -       ID:AN.73651.45446.R.AP.07UR     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.08.1.P.fq   AN.73651.45446.R.AP.08.2.P.fq   ID:AN.73651.45446.R.AP.08       SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.08.1.U.fq   -       ID:AN.73651.45446.R.AP.08UF     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
AN.73651.45446.R.AP.08.2.U.fq   -       ID:AN.73651.45446.R.AP.08UR     SM:UMCUSAM000000073651  LB:d    PL:ILLUMINA
alexdobin commented 1 year ago

Hi Bob,

indeed, STAR cannot map a mixture of SE and PE reads, you would need to map them separately.