Thanks for developing RNAEditor. I have been trying to use it on human single-cell RNA-Seq data. So far I could get it to work by creating a conda environment so that everything runs with python2.7. But, I am stuck at bwa mapping, as it has problems with converting sai to sam files. Attached is the log file.
ERR1630013.log
However, when I manually convert the sai to sam file using the bwa installed in usr/local/bin, it works perfectly.
Dear David
Thanks for developing RNAEditor. I have been trying to use it on human single-cell RNA-Seq data. So far I could get it to work by creating a conda environment so that everything runs with python2.7. But, I am stuck at bwa mapping, as it has problems with converting sai to sam files. Attached is the log file. ERR1630013.log
However, when I manually convert the sai to sam file using the bwa installed in usr/local/bin, it works perfectly.
(RNA_Edit) sumeet@sumeet-HP-350-G2 ~/Downloads/testRNAEditing/rnaEditor/ERR1630013 $ /usr/local/bin/bwa samse /home/sumeet/Documents/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ERR1630013.sai ../../ERR1630013.fq > ERR1630013.sam [bwa_aln_core] convert to sequence coordinate... 4.52 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.01 sec [bwa_aln_core] 17947 sequences have been processed. [main] Version: 0.7.17-r1194-dirty [main] CMD: /usr/local/bin/bwa samse /home/sumeet/Documents/GRCH38/Homo_sapiens.GRCh38.dna.primary_assembly.fa ERR1630013.sai ../../ERR1630013.fastq [main] Real time: 41.261 sec; CPU: 5.116 sec
I am wondering if there is some issue on my side that is leading to this error.
Thanks, Sumeet