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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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Cuffquant errors after using HISAT2 #58

Closed alisaberi92 closed 8 years ago

alisaberi92 commented 8 years ago

Hi Dear Dr. Kim, I have 2 sequence reads archive and I want to do some RNA-Seq analysis on them. Archive 1 : SRR1177960 (FastQ Files : SRR1177960_1, SRR1177960_2) Archive 2 : SRR1177961 (FastQ Files : SRR1177961_1, SRR1177961_2) I aligned both archives using HISAT2, and I got the results (BAM files). Then I pass the results of each archive separately to Cufflinks, and I got the results (GTF files). Then I pass the results to Cuffmerge, and I got the result (GTF file). Then I pass the Cuffmerge result + HISAT2 result of archive 1 to the Cuffquant, and I got the result (CXB file). BUT when I pass the Cuffmerge result + HISAT2 result of archive 2 to the Cuffquant, I got error BAM record error: found spliced alignment without XS attribute I attached the full text of error : cuffquant_error_archive2.txt Can you help me? (I forgot to say that I'm using Galaxy (usegalaxy.org)) Thanks.

infphilo commented 8 years ago

I believe this issue was fixed in the recent versions of HISAT2.