Hello,
I am new to this field and this is the first time I am using Bowtie2. I installed Bowtie2 and created the index files for Hg19. (I tried a SET file and it maps without a problem)
I want to align a paired end tag data set. I downloaded the CTCF PET dataset from http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR525042 and created the two fastq files using SRATools.
Then I used the following command in Bowtie2.
But I am getting almost zero map. I tried using --ff/--fr/--rf but no luck so far.
Any help would be appreciated. Thanks in advance.
I am new to this field and this is the first time I am using Bowtie2. I installed Bowtie2 and created the index files for Hg19. (I tried a SET file and it maps without a problem)
I want to align a paired end tag data set. I downloaded the CTCF PET dataset from http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR525042 and created the two fastq files using SRATools.
Then I used the following command in Bowtie2.
Code:
/home/Bowtie2/bowtie2-2.2.2/bowtie2 -x /home/Hg19/Reference/humanGenome -1 /scratch/PET/SRR525042_1.fastq -2 /scratch/PET/SRR525042_2.fastq -S CTCFFinal.sam
Any help would be appreciated. Thanks in advance.
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