abedkurdi
commented
1 year ago The problem here is in the chromosomes names: as you can see here the first contig name:
reads contigs = [1_dna:chromosome_chromosome:GRCh38:1:1:248956422:1_REF
and the contig name in the reference fasta is: 1.
If you check the contigs names in your reference fasta, I am sure you will see the following (for chromosome 1):
1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF.
The problem is that during the step of reference bisulfitation, any spaces in the contig name are converted into underscores. If you replace the spaces in the contig names with underscores, your problem will be solved.
Hello to everyone,
in my new lab I have been given some files from a bisulphite targeted sequencing, with only a few genes. I am new to analysing this kind of results and I am trying to do it with BICYCLE, but I am having some problems. I have four ".FASTQ" sequences with these names:
_Undetermined_S0_L001_R1_001.fastq 1_S1_L001_R1_001.fastq Undetermined_S0_L001_R1_001.fastq 1_S1_L001_R2_001.fastq 1_S1_L001_R1_001.fastq 1_S1_L001_R1_001.fastq 1_S1_L001_R1_001.fastq 1_S1_L001_R2001.fastq
I don't really know what the "Undetermined" sequences are, but they take up about 15 GB, while the other two are quite small, about 7 MB uncompressed. I know that I have to use these and that they are paired, hence the "R1" and "R2" and that I need a reference genome, for which I downloaded this one:.
With this, I have simply tried to combine the information from the "Quick start" tutorial, with the "Case study" tutorial to do my analysis, I have been able to complete without problems. So with my samples I was also able to complete the following steps: Create project, Create bisulphite version of the genome, Create reference index and Align reads; but when I get to the methylation analysis, I get the following error:
My theory is that the problem is because it didn't manage to align anything with the ".bam" files, mainly because of what I get when I run this code:
Maybe the problem is because the files I have been given are not of high enough quality, but then I don't understand why it has generated ".bam" files in the first place (and the weirdest thing is that these files are not 0 B but 7,3 kB in size). What do you think is the problem?
Thank you very much in advance and sorry for this first long query, but I've been trying for a few weeks now and I don't know what to do.