Closed timedreamer closed 6 years ago
Could you share your bam files?
Sure. Here is the google drive link for the two bam files.
The STAR command I used is this:
STAR --genomeDir {STARREF} --readFilesCommand zcat \
--readFilesIn {input.r1} {input.r2} \
--outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 \
--outSAMunmapped Within --twopassMode Basic --outFilterMultimapNmax 10 \
--quantMode GeneCounts --outReadsUnmapped None --outSAMstrandField intronMotif \
--chimOutType SeparateSAMold --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 \
--alignMatesGapMax 100000 --alignIntronMax 100000 --chimSegmentReadGapMax 3\
-alignSJstitchMismatchNmax 5 -1 5 5 \
--runThreadN {threads} --outFileNamePrefix '../data/star_output/{wildcards.sample}'
Thanks for your time!
The latest release should fix that error. Please check out to see whether the latest version works, or whether there are new problems.
Works fine now. Thanks!
Hi,
My SQUID run returned this error. Any ideas?
Return:
Many thanks.
Ji