Trying to figure out what the last line is of samtools idxstats output:
Here are the last few lines,
GL456368.1 20208 266 0
JH584292.1 14945 8 0
JH584295.1 1976 31 0
* 0 0 33800462
Is this an additional unmapped region? Attempted to get the bam file however was unable, not sure of proper notation for samtools view
samtools view -b /Users/possorted_genome.bam * > asterisk.bam
Basic point is looking for a randomly integrated human transgene in a mouse snRNA-seq assembly.
Also can a transgene integrate potentially within an unplaced contig like the ones above, was able to find mouse version of gene by blasting a db of chromosome 13 from mapped reads - but can't find the human even though I know its there.
Thanks.
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LacquerHed •
Is it possible to just convert all unmapped reads to a bam file, covert to fasta and just blast that for the transgene? When trying with samtools view I couldn't figure out the right notation. Im guessing it should be there, and seems less involved than augmenting the assembly. Thanks!
to get unmapped reads from a bam file you can use:
samtools view -f 4 file.bam
you can then blast the sequences
A more proper way would be to add your transgene to your reference as suggested by ATpoint, as there could be reads mapping to both (possibly with some mismatch)
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If you are looking for a genomic insertion site then it may be better to follow the protocol described in this answer: Identification of the sequence insertion site in the genome