I have Illumina data that was spiked with PhiX sequences as an internal control, and I'd like to make sure those sequences are removed from my data before I try assembling it. I thought of using Bowtie and saving the unmapped reads, but I'm not sure Bowtie would produce the right output or that I have correctly formatted input files.
I have trimmed fastq files for input, unpaired end reads since the pairs are not interleaved and have been disrupted by trimming and discarding too-short sequences. They aren't in tab-delimited format- is there a handy tool to convert them? I am not much good at coding.
I have the PhiX genome in Fasta format and plan to use Bowtie-build to make an index that can be used with Bowtie.
If I use the --un option, I can save reads that did not align, which are the ones I want to keep- they will be in tab-delimited format, and I will need to re-convert them back to fastq format? (I plan to use them with Trinity, which uses fastq as its input format).
Thanks for any help you can provide,
Liz
I have trimmed fastq files for input, unpaired end reads since the pairs are not interleaved and have been disrupted by trimming and discarding too-short sequences. They aren't in tab-delimited format- is there a handy tool to convert them? I am not much good at coding.
I have the PhiX genome in Fasta format and plan to use Bowtie-build to make an index that can be used with Bowtie.
If I use the --un option, I can save reads that did not align, which are the ones I want to keep- they will be in tab-delimited format, and I will need to re-convert them back to fastq format? (I plan to use them with Trinity, which uses fastq as its input format).
Thanks for any help you can provide,
Liz
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