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1. Tophat produced accepted_hits.bam
2. samtools index produced accepted_hits.bam.bai
3. samtools view produced accepted_hits.sam
4. cufflinks -g reference.gff -o output_file accepted_hits.sam
Right after typing cufflinks command,
the messages appeared like the following:
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File accepted_hits.sam doesn't appear to be a valid BAM file, trying SAM...
Are these messages okay and will there be no problem in output?
Thanks in advance.
2. samtools index produced accepted_hits.bam.bai
3. samtools view produced accepted_hits.sam
4. cufflinks -g reference.gff -o output_file accepted_hits.sam
Right after typing cufflinks command,
the messages appeared like the following:
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File accepted_hits.sam doesn't appear to be a valid BAM file, trying SAM...
Are these messages okay and will there be no problem in output?
Thanks in advance.