Hi all,
Excuse my newbie-ness as I typically work within the DNA realm but decided to do an expression analysis for a final project in my Genomics class. Anyways, I have all the reads and the reference transcriptome downloaded and for part 1 of the analysis I am trying to map read data back to the reference transcriptome. Here are the codes that I used:
bowtie2-2.2.4/bowtie2-build 33496_Ahyacinthus_CoralContigs.fasta hg19
bowtie2-2.2.4/bowtie2 -p 6 -x hg19 06_control_HV_100000.fastq > 6controlHV.sam
100000 reads; of these:
100000 (100.00%) were unpaired; of these:
77030 (77.03%) aligned 0 times
20885 (20.89%) aligned exactly 1 time
2085 (2.08%) aligned >1 times
22.97% overall alignment rate
As you can see, the overall alignment rate is quite low. I have tried changing various parts of the code with no luck. Am I executing this in the wrong way/is there something that I am missing?
Thanks in advance.
Excuse my newbie-ness as I typically work within the DNA realm but decided to do an expression analysis for a final project in my Genomics class. Anyways, I have all the reads and the reference transcriptome downloaded and for part 1 of the analysis I am trying to map read data back to the reference transcriptome. Here are the codes that I used:
bowtie2-2.2.4/bowtie2-build 33496_Ahyacinthus_CoralContigs.fasta hg19
bowtie2-2.2.4/bowtie2 -p 6 -x hg19 06_control_HV_100000.fastq > 6controlHV.sam
100000 reads; of these:
100000 (100.00%) were unpaired; of these:
77030 (77.03%) aligned 0 times
20885 (20.89%) aligned exactly 1 time
2085 (2.08%) aligned >1 times
22.97% overall alignment rate
As you can see, the overall alignment rate is quite low. I have tried changing various parts of the code with no luck. Am I executing this in the wrong way/is there something that I am missing?
Thanks in advance.
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