BAM Record Error
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I am trying to use SEASTAR on human RNASeq data. My inputs are BAM files aligned with STAR. They are single-end, reverse strand reads (sequenced on Illumina HiSeq 2500). Whenever I try to run "SEASTAR.sh", I get an error message that says "BAM record error: found spliced alignment without XS attribute" when SEASTAR is at the "Process locus: " stage. I am using the following command:
bash /home/travisblimkie/bin/SEASTAR-master/SEASTAR.sh
-A /mnt/analysis1/myproj/STAR_files/sample1_Aligned.sortedByCoord.out.bam
-B /mnt/analysis1/myproj/STAR_files/sample4_Aligned.sortedByCoord.out.bam
-o /mnt/analysis1/myproj/Seastar_runs/sample1
-g /mnt/analysis1/Genomes/Human_GRCh38_bowtie_index/Homo_sapiens.GRCh38.93.gtf
-i /mnt/analysis1/Genomes/Human_GRCh38_bowtie_index/human.chrom.sizes
-s /mnt/analysis1/Genomes/Human_GRCh38_bowtie_index/Homo_sapiens.GRCh38.dna.primary_assembly.fa
-S s
From a quick search online, it seems like it has something to do with incorrect parameters being given to cufflinks. Any suggestions would be greatly appreciated.
Thanks,
Travis
Fixed this issue by modifying the "gtf.sh" and "tsgtf.sh" scripts to include the "--library-type fr-firststrand" option in the call to cufflinks