Same issue
Hey guys
I'm having the same issue. When I run Cufflinks this is what I get
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File /Users/sohailkhan/Documents/MiSeq_data/12082014_CLIP/untag_sorted doesn't appear to be a valid BAM file, trying SAM...
[12:24:10] Loading reference annotation.
[12:24:11] Inspecting reads and determining fragment length distribution.
> Processing Locus AB325691:1478-3197 [ ] 0%SAM error on line 49: found spliced alignment without XS attribute
> Processing Locus I:27352-27763 [**** ] 16%SAM error on line 380: found spliced alignment without XS attribute
SAM error on line 381: found spliced alignment without XS attribute
SAM error on line 384: found spliced alignment without XS attribute
> Processing Locus I:29763-31069 [**** ] 16%SAM error on line 474: found spliced alignment without XS attribute
SAM error on line 479: found spliced alignment without XS attribute
SAM error on line 480: found spliced alignment without XS attribute
SAM error on line 481: found spliced alignment without XS attribute
SAM error on line 482: found spliced alignment without XS attribute
SAM error on line 485: found spliced alignment without XS attribute
SAM error on line 486: found spliced alignment without XS attribute
SAM error on line 488: found spliced alignment without XS attribute
SAM error on line 489: found spliced alignment without XS attribute
> Processing Locus I:45874-48399 [**** ] 16%SAM error on line 603: found spliced alignment without XS attribute
SAM error on line 604: found spliced alignment without XS attribute
I used the latest STAR release for Mac and I'm using the latest release of Cufflinks. The STAR options I used were:
--runThreadN 6 --outSJfilterOverhangMin 30 10 10 10
--outFilterMismatchNmax 6 --alignIntronMin 10 --alignIntronMax 500 --alignMatesGapMax 500 --alignSplicedMateMapLmin 1 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonical --sjdbGTFfile /PATH --sjdbOverhang 74
Is there any option I need to add for the right XS attributes?
Originally posted by bob-loblaw
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I'm having the same issue. When I run Cufflinks this is what I get
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File /Users/sohailkhan/Documents/MiSeq_data/12082014_CLIP/untag_sorted doesn't appear to be a valid BAM file, trying SAM...
[12:24:10] Loading reference annotation.
[12:24:11] Inspecting reads and determining fragment length distribution.
> Processing Locus AB325691:1478-3197 [ ] 0%SAM error on line 49: found spliced alignment without XS attribute
> Processing Locus I:27352-27763 [**** ] 16%SAM error on line 380: found spliced alignment without XS attribute
SAM error on line 381: found spliced alignment without XS attribute
SAM error on line 384: found spliced alignment without XS attribute
> Processing Locus I:29763-31069 [**** ] 16%SAM error on line 474: found spliced alignment without XS attribute
SAM error on line 479: found spliced alignment without XS attribute
SAM error on line 480: found spliced alignment without XS attribute
SAM error on line 481: found spliced alignment without XS attribute
SAM error on line 482: found spliced alignment without XS attribute
SAM error on line 485: found spliced alignment without XS attribute
SAM error on line 486: found spliced alignment without XS attribute
SAM error on line 488: found spliced alignment without XS attribute
SAM error on line 489: found spliced alignment without XS attribute
> Processing Locus I:45874-48399 [**** ] 16%SAM error on line 603: found spliced alignment without XS attribute
SAM error on line 604: found spliced alignment without XS attribute
I used the latest STAR release for Mac and I'm using the latest release of Cufflinks. The STAR options I used were:
--runThreadN 6 --outSJfilterOverhangMin 30 10 10 10
--outFilterMismatchNmax 6 --alignIntronMin 10 --alignIntronMax 500 --alignMatesGapMax 500 --alignSplicedMateMapLmin 1 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonical --sjdbGTFfile /PATH --sjdbOverhang 74
Is there any option I need to add for the right XS attributes?
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