Hello,
I am very new to using Bowtie2, and would love some help!
I am hoping to do a paired end alignment. I had the same number of sequences in each file originally. First, I did a quality trim using FASTX to remove low quality sequence at the end. Then, when I try to do my paired end alignment, I get an error message saying that I had a different number of sequences in the two files. I'm guessing that perhaps one (or more) of my sequences was of a low quality all the way through and removed altogether...?
What is the best way around this problem? Is there an option in Bowtie2 to deal with an unequal number of sequences?
Thanks so much!
I am very new to using Bowtie2, and would love some help!
I am hoping to do a paired end alignment. I had the same number of sequences in each file originally. First, I did a quality trim using FASTX to remove low quality sequence at the end. Then, when I try to do my paired end alignment, I get an error message saying that I had a different number of sequences in the two files. I'm guessing that perhaps one (or more) of my sequences was of a low quality all the way through and removed altogether...?
What is the best way around this problem? Is there an option in Bowtie2 to deal with an unequal number of sequences?
Thanks so much!
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