Hi there,
I'm a bit of a noob and feel somewhat stupid for asking this question, but here goes...
When using coverageBed I end up with a blank text file....
My analysis pipeline is as follows:
- bowtie2 to align paired end fastq files (miseq) to indexed fasta file
bowtie2 -x $file -1 $file.fastq -2 $file.fastq -S $file.sam
- samtools to convert sam to bam
samtools view -bS $file.sam> $file.bam
- bedtools to produce a coverage file
coverageBed -abam $file.bam -b $.bed > $file.txt
The resulting text file comes out completely empty.
Ive tried using the .bam and .bed file in bedtools implemented through Galaxy using count of overlaps, and it works.
Anyone have any ideas? Feel like such an idiot getting stuck at such an early stage
First few lines of me .bed file
chr16 3777645 3777833 CREBBP_1
chr16 3777843 3778042 CREBBP_3
chr16 3778025 3778199 CREBBP_5
chr16 3778174 3778368 CREBBP_8
chr16 3778339 3778532 CREBBP_10
chr16 3778566 3778763 CREBBP_12
chr16 3778725 3778875 CREBBP_14
Many thanks for the help!
I'm a bit of a noob and feel somewhat stupid for asking this question, but here goes...
When using coverageBed I end up with a blank text file....
My analysis pipeline is as follows:
- bowtie2 to align paired end fastq files (miseq) to indexed fasta file
bowtie2 -x $file -1 $file.fastq -2 $file.fastq -S $file.sam
- samtools to convert sam to bam
samtools view -bS $file.sam> $file.bam
- bedtools to produce a coverage file
coverageBed -abam $file.bam -b $.bed > $file.txt
The resulting text file comes out completely empty.
Ive tried using the .bam and .bed file in bedtools implemented through Galaxy using count of overlaps, and it works.
Anyone have any ideas? Feel like such an idiot getting stuck at such an early stage
First few lines of me .bed file
chr16 3777645 3777833 CREBBP_1
chr16 3777843 3778042 CREBBP_3
chr16 3778025 3778199 CREBBP_5
chr16 3778174 3778368 CREBBP_8
chr16 3778339 3778532 CREBBP_10
chr16 3778566 3778763 CREBBP_12
chr16 3778725 3778875 CREBBP_14
Many thanks for the help!
Comment