How to compare de novo and reference mappings in SNPs analysis?
Hello. I am a beginner in this field and I have a question, sorry if it is obvious !
In SNPs analysis (by Stacks software) with FASTQ sample files (from Illumina), I perform 2 different analyses:
– the first one is a reference mapping: the FASTQ sample files are aligned with a FASTA genome file by Bowtie or BWA softwares, then the SAM result files are analysed by Stacks and a TSV text result file is generated (with informations like chromosome and base positions, consensus sequences, SNPs, alleles variations, etc.);
– the second one is a de novo mapping: the FASTQ sample files are directly analysed by Stacks and a TSV result file is generated (with the same informations as first case);
I would like to compare the results of these 2 analyses (reference versus de novo).
Firstly, I sorted the lines inside the 2 result files (keeping only the consensus sequence informations) and performed a text comparison with Meld software, but this method has one weaknesse: one difference in the consensus sequence will result in a total mismatch…
Secondly, I generated a FASTA file from the de novo's TSV result file which was analysed after by the same aligner as first case (Bowtie or BWA, generating a SAM result file), in order to obtain position informations, and again I sorted the files (keeping only the consensus sequences and position informations) and performed a comparison with Meld, but again this method has some weaknesses: a small difference in consensus sequence or in the position (on the same chromosome, for example) will also result in a total mismatch… I also noticed that many matching sequences have a position difference of 1 base for the exactly same consensus sequence…
I would like to know if there are softwares which can help me, for example by making an alignment between the short sequences of these 2 files (SAM or TSV/CSV text files), if possible taking into account the position informations (obtained from the first alignment with a reference genome: chromosome and base position), without forgetting that my purpose is to compare results in SNPs analysis.
Thank you very much for your time and your potential help.
Sincerely yours.
In SNPs analysis (by Stacks software) with FASTQ sample files (from Illumina), I perform 2 different analyses:
– the first one is a reference mapping: the FASTQ sample files are aligned with a FASTA genome file by Bowtie or BWA softwares, then the SAM result files are analysed by Stacks and a TSV text result file is generated (with informations like chromosome and base positions, consensus sequences, SNPs, alleles variations, etc.);
– the second one is a de novo mapping: the FASTQ sample files are directly analysed by Stacks and a TSV result file is generated (with the same informations as first case);
I would like to compare the results of these 2 analyses (reference versus de novo).
Firstly, I sorted the lines inside the 2 result files (keeping only the consensus sequence informations) and performed a text comparison with Meld software, but this method has one weaknesse: one difference in the consensus sequence will result in a total mismatch…
Secondly, I generated a FASTA file from the de novo's TSV result file which was analysed after by the same aligner as first case (Bowtie or BWA, generating a SAM result file), in order to obtain position informations, and again I sorted the files (keeping only the consensus sequences and position informations) and performed a comparison with Meld, but again this method has some weaknesses: a small difference in consensus sequence or in the position (on the same chromosome, for example) will also result in a total mismatch… I also noticed that many matching sequences have a position difference of 1 base for the exactly same consensus sequence…
I would like to know if there are softwares which can help me, for example by making an alignment between the short sequences of these 2 files (SAM or TSV/CSV text files), if possible taking into account the position informations (obtained from the first alignment with a reference genome: chromosome and base position), without forgetting that my purpose is to compare results in SNPs analysis.
Thank you very much for your time and your potential help.
Sincerely yours.