Rsamtools Bam file reading error

[dab32]

Hi,

I aligned Illumina and also SOLiD (colour space) data files separately using bowtie (version 0.12.7), and I also filtered unmapped reads, sorted and converted sam to bam files using samtools (0.1.4) and the following commands:

Example of illumina commands:

bowtie database_name file1.fastq --sam -q -v 0 -m 1 > file1.sam
samtools view -bS -F 4 -o file1_unsorted.bam file1.sam
samtools sort file1_unsorted.bam file_1
samtools index file_1.bam

I get the following error message when I read bam.file into R using RSamtools... " EOF marker is absent. The input is probably truncated."

However, this happens only with Illumina files and not with SOLiD.
Interestingly, the number of reads seems to be the same as in the sam file and the bam file seem to be intact. I can get the data from the RangedData object in R with no problems whatsoever

I searched several forums including this one and some suggest simply to ignore this message

I wondered whether I should ignore this error message, or maybe there is something wrong with the commands above

Many thanks for your help,

Danny