Hello all,
I have been having trouble generating consensus files from sorted BAM files.
I have tried both the mpileup command-
samtools mpileup -uf ./genomes/NC_013316.fna 2245.sorted.bam | ../samtools-0.1.16/bcftools/bcftools view -cg - | ../samtools-0.1.16/bcftools/vcfutils.pl vcf2fq > 2245cns.fq
and the depreciated pileup command -
samtools pileup -cf ./genomes/NC_013316.fna 2245.sorted.bam | ../samtools-0.1.16/misc/samtools.pl pileup2fq -D150 > 2245pcns.fastq
Both commands run correctly, however when I look at the fastq file it truncates at line 69857 and the rest of the files is filled with this character ( ~~~~) and random letters, as shown below -
TCCATAAATTTAGTTATTCTGTAAAATTTATATATATTTTTGCTTTTCTGTTAATAACTT
TGTGGAAAATATTAATTATTCTGTTCGGAGGTTTATatt
+
?BBEEEEHNNNNNZZ`ccffiiloru~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Can anyone please explain what may be going on?
I am very new to seq analysis and can't work it out!
Emma
I have been having trouble generating consensus files from sorted BAM files.
I have tried both the mpileup command-
samtools mpileup -uf ./genomes/NC_013316.fna 2245.sorted.bam | ../samtools-0.1.16/bcftools/bcftools view -cg - | ../samtools-0.1.16/bcftools/vcfutils.pl vcf2fq > 2245cns.fq
and the depreciated pileup command -
samtools pileup -cf ./genomes/NC_013316.fna 2245.sorted.bam | ../samtools-0.1.16/misc/samtools.pl pileup2fq -D150 > 2245pcns.fastq
Both commands run correctly, however when I look at the fastq file it truncates at line 69857 and the rest of the files is filled with this character ( ~~~~) and random letters, as shown below -
TCCATAAATTTAGTTATTCTGTAAAATTTATATATATTTTTGCTTTTCTGTTAATAACTT
TGTGGAAAATATTAATTATTCTGTTCGGAGGTTTATatt
+
?BBEEEEHNNNNNZZ`ccffiiloru~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Can anyone please explain what may be going on?
I am very new to seq analysis and can't work it out!
Emma
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