Seeing only "N's" in tablet genome viewer?
I downloaded a bam file of an exome sequence from the 1000 genome project website and ran samtools view to extract chromosome 22. My command was
samtools view -b NA20515.bam 22 > chr22.bam
I received the message random alignment retrieval only works for indexed BAM or CRAM files but it still created a bam file nonetheless that was 5 kb in size. I then ran samtools index chr22.bam to create the indexed bam file. I want to map the reads in Tablet genome viewer, so I load the chr22 bam file with the reference genome in Tablet, but when I visualize all of the reads in tablet all I see are N's. Did I do something wrong with samtools?
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Did you check by doing
samtools view chr22.bam | lessto make sure there are actually alignments in it? Perhaps you only created a file with the header, which is otherwise empty.If it's only header, s/he needs
samtools view -h chr22.bamto see the headerHow would I know that it actually has alignments in it?
You should see lines like this (apologies for borrowing the data from a recent unrelated thread)
do you have the file
NA20515.bam.bai?yes, the bai file is in the same directory