Question: Cufflinks invalid BAM binary header
0
gravatar for murphy.charlesj
3.7 years ago by
United States
murphy.charlesj90 wrote:

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).

rna-seq • 2.0k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by murphy.charlesj90

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 samtols page
Bam Header Edit

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Sukhdeep Singh9.7k

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

 

ADD REPLYlink written 3.7 years ago by murphy.charlesj90

run

file Sample_het1.Aligned.sortedByCoord.out.bam

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

 

 

ADD REPLYlink written 3.7 years ago by Pierre Lindenbaum119k

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
ADD REPLYlink written 3.7 years ago by murphy.charlesj90
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