Filtered reads from assembly and raw reads?

Question

[el97004]

Hi all!

Anyone know of a software tool that can be used to get reads from a de-novo assembly if I have the raw reads? the raw reads went through several steps of preprocessing and filtering and I no longer have the final reads that were used to make the assembly.

Thank you!

Answer 1

[GenoMax]

can be used to get reads from a de-novo assembly if I have the raw reads?

If you have an assembly then the individual reads are no longer identifiable since they are now part of a long sequence.

If you are looking to see which part of an assembly a read may belong to then you can simply align the reads to the assembly.

[el97004]

Thanks GenoMax ! Once aligned and obtained bam file could I not then just convert that to fastq?

[GenoMax]

Not sure then what your question is. What format is your query data in? That must already be in fastq format? Are you simply looking to extract reads that align to the assembly then (sometimes all reads may not align)?

[el97004]

Yeah I was just trying to find the set of reads that were used to make up the final assembly. Some of those raw reads will definitely not align since they were filtered out (e.g. contaminants).

Format information: assembly: fasta; raw reads: fastq

[GenoMax]

In that case use an aligner of your choice and extract reads that map: How To Filter Mapped Reads With Samtools

Be sure to get primary alignments (otherwise) there may be multiple copies of reads in extract.