[solved] Bowtie mapping paired-end reads of different length
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5.0 years ago
biostart ▴ 360

Hello,

For technical reason one set of reads is sequences to 100bp, and another set of reads from the same pair is sequences at 80 bp (that is, in the same pair one read is 80 bp and another one is 100 bp). Is it a problem if I just start mapping them with Bowtie as they are, or additional manipulations are needed?

PS. I tried mapping wing Bowtie without trimming and it gives 0 mapped reads so far.

What is the way to process an unmapped fastq file to have both files sequenced 80 bp?

ChIP-Seq • 2.0k views
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Are you using bowtie2 (hopefully not bowtie1)? Uneven lengths should not cause a problem.

-1 <m1>

Comma-separated list of files containing mate 1s (filename usually includes _1), e.g. -1 flyA_1.fq,flyB_1.fq. Sequences specified with this option must correspond file-for-file and read-for-read with those specified in <m2>. Reads may be a mix of different lengths. If - is specified, bowtie2 will read the mate 1s from the "standard in" or "stdin" filehandle.

-2 <m2>

Comma-separated list of files containing mate 2s (filename usually includes _2), e.g. -2 flyA_2.fq,flyB_2.fq. Sequences specified with this option must correspond file-for-file and read-for-read with those specified in <m1>. Reads may be a mix of different lengths. If - is specified, bowtie2 will read the mate 2s from the "standard in" or "stdin" filehandle.

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I am actually using bowtie1 :(

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Bowtie1 manual also says the same. So the problem must be something else.
Have you tried to take a few reads and confirm by blasting at NCBI that they are aligning to the right genome?

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solved! I started another bowtie version, and it's running and finding reads

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