Cufflinks invalid BAM binary header

Question

[murphy.charlesj]

I get this warning when running cufflinks on my RNA-seq. Does not prevent me from doing my analysis, I' am just curious what it is. In short, I have paired end RNA-seq mapped with STAR (v2.4.1d) against GRCm38.

STAR \
  --outSAMtype BAM SortedByCoordinate \
  --runThreadN 8 \
  --outSAMstrandField intronMotif \
  --genomeDir ./GRCm38/star \
  --readFilesIn [fastqfiles] \
  --readFilesCommand zcat \
  --outFileNamePrefix Sample_het1.

Then quantify with cufflinks (v2.2.1).

cufflinks \
  -q \
  -p 8 \
  -o ./ \
  -b Mus_musculus.GRCm38.dna.primary_assembly.fa \
  -G Mus_musculus.GRCm38.79.gtf Sample_het1.Aligned.sortedByCoord.out.bam

I get the following message

[bam_header_read] invalid BAM binary header (this is not a BAM file)

[Sukhi Singh]

Try samtools view to see if the header is present.

You can try to rehead the file using reheader

Check the syntax here or on the samtools page Bam Header Edit

[murphy.charlesj]

Indeed there is, here are the first few lines:

@HD    VN:1.4    SO:coordinate
@SQ    SN:1    LN:195471971
@SQ    SN:10    LN:130694993
@SQ    SN:11    LN:122082543
@SQ    SN:12    LN:120129022
@SQ    SN:13    LN:120421639

[Pierre Lindenbaum]

Run

file Sample_het1.Aligned.sortedByCoord.out.bam

If it doesn't say it's a "gzip" file, then it's NOT bam.

[murphy.charlesj]

Ran the command and its says it is a gzip file

file Sample_het1.Aligned.sortedByCoord.out.bam
Sample_het1.Aligned.sortedByCoord.out.bam: gzip compressed data, extra field