Hi all,
Someone in our lab just got finished with sequencing and assembly of a number of contigs. The question was asked, whether or not she found HiSeq to be useful, or if we could use MiSeq in the future.
I thought if I could align the reads onto her contigs, then we could assess the coverage, and possibly whether or not HiSeq was necessary.
I found that Bowtie allows you to align short reads to a reference sequence.
I concatenated the FASTA files for all the contigs and successfully made a bowtie2 index from the file.
Now, I'm trying to map the paired-end reads onto the index:
but keep coming up with the error
What am I doing wrong?
Someone in our lab just got finished with sequencing and assembly of a number of contigs. The question was asked, whether or not she found HiSeq to be useful, or if we could use MiSeq in the future.
I thought if I could align the reads onto her contigs, then we could assess the coverage, and possibly whether or not HiSeq was necessary.
I found that Bowtie allows you to align short reads to a reference sequence.
I concatenated the FASTA files for all the contigs and successfully made a bowtie2 index from the file.
Now, I'm trying to map the paired-end reads onto the index:
Code:
./bowtie2 -S -p 2 DscP_kaster -1 KM01_GW1_TAAGGCGA_L005_R1_001.fastq -2 KM01_GW1_TAAGGCGA_L005_R2_001.fastq KM01_bowtie.sam
Code:
bowtie2-align exited with value 1
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