More posts like this
-
Does this adapter content from fastqc to warrant trimming prior to alignment?
written by curious
-
What can cause broken read-pairs (chimeric read-pairs) in a sequencing run?
written by William
-
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
written by Ben •
-
Same gene_id on different chromosome in hg19 known gene gtf file
written by jli2274 •
-
Pindel: long run-time and low CPU usage
written by Lillian •
-
DEGs with uninsteresed sample files
written by jkim •
-
STAR vs Novoalign IGV Browser visualization
written by chasem •
-
Handling RNA-seq samples from the same individual in DEseq2 analysis
written by gspirito •
-
quantile normalization in deseq2
written by bioinfo456
-
ground truth dataset for BAM read counts
written by Marius •
Are you sure they use the same reference?
The same person, different samples.
@German is asking if the data from two samples is aligned to an identical reference.
hg19 vs hg38
trying to covert the hr19 to hr38 with no luck so far.
CrossMap.py bam -a ./hg19ToHg38.over.chain.gz ./t.bam ./t.hg38
Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/bin/CrossMap.py", line 1744, in <module> crossmap_bam_file(mapping = mapTree, chainfile = chain_file, infile = in_file, outfile_prefix = out_file, chrom_size = targetChromSizes, IS_size=options.insert_size, IS_std=options.insert_size_stdev, fold=options.insert_size_fold,addtag=True) File "/Library/Frameworks/Python.framework/Versions/2.7/bin/CrossMap.py", line 827, in crossmap_bam_file (new_header, name_to_id) = sam_header.bam_header_generator(orig_header = sam_ori_header, chrom_size = chrom_size, prog_name="CrossMap",prog_ver = __version__, format_ver=1.0,sort_type = 'coordinate',co=comments) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cmmodule/sam_header.py", line 27, in bam_header_generator bamHeaderLine['HD'] = {'VN':format_ver,'SO':sort_type} File "pysam/libcalignmentfile.pyx", line 545, in pysam.libcalignmentfile.AlignmentHeader.__setitem__ TypeError: AlignmentHeader does not support item assignment (use header.to_dict()
It would be best to convert the data back to fastq files and remap it in both cases to a reference you know. Otherwise the comparison you are trying to make may not be useful. There can be subtle differences in how data is mapped/processed and doing a simple crossmap may not be sufficient to do a meaningful comparison.
Thanks I have both original fastq files but they are split into two, do I need to merge them first?
As in they are from two lanes e.g. have
L001orL002etc in their names? They can be processed in parallel for each sample and then merged at BAM step. You could alsocatthem together in same order forR1/R2files before aligning.yes, if these are 2 very different reference genomes - this is what expected
I agree with GenoMax that they'd be better transformed to fastq rather than lifted over
thanks for the help