Error in Generating sorted.bam
Hi all, I posted a question few weeks back and I haven't been able to resolve the issue with my .Bam and sorted.bam files.
I ran the following command and for some reason, I can't generate my required files which I need for running the GATK command. (my reference genome is an index file). also, I'm a Beginner.
$ bowtie2 -x /Volumes/500GB/pavelAssemblyBowtieIndex -1/Volumes/500GB/Illumina_Run_814/Run_814/Project_klimov/Sample_28017/28017_GTCCGC_L006_R1_001.fastq -2 /Volumes/500GB/Illumina_Run_814/Run_814/Project_klimov/Sample_28017/28017_GTCCGC_L006_R2_001.fastq -S dustMapping.sam && samtools view -S -b dustMapping.sam -o dustMapping.bam && samtools sort dustMapping.bam -odustMapping.sorted.bam && samtools index dustMapping.sorted.bam -o dustMapping.sorted.bam.bai && rm dustmapping.sam && dustmapping.bam
(ERR): "/Volumes/500GB/pavelAssemblyBowtieIndex" does not exist or is not a Bowtie 2 index
Exiting now ...
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Are all of your index files prefixed with 'pavelAssemblyBowtieIndex' and in the
/Volumes/500GB/folder? Cause that's what it's looking for -/Volumes/500GB/pavelAssemblyBowtieIndex.1.bt2, etc, and it can't find them.Also, the
-oargument isn't needed forsamtools index, it'll create the new file with the extension as you have it without the argument.All the bt2 are in the pavel folder. I would have used the reference genome but I only have the indexes.
Could you get the dustMapping.sam that is the first output file?
If not, please check whether there are bowtie"2" index files near the reference file (pavelAssemblyBowtieIndex .fa).
Bowtie2 index : .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, and .rev.2.bt2.
Bowtie 2's .bt2 index format is different from Bowtie 1's .ebwt format, and they are not compatible with each other.
http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
Ok let me go ahead and run only the sam output. But there is no .fa file. I only have the indexes.