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8.5 years ago
tonja.r
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600
According to samtools:
Important note: when multiple regions are given, some alignments may be output multiple times if they overlap more than one of the specified regions. However, if I have such a bed file:
chr1 3033215 3044215 ENSMUSG00000090025.1/Gm16088 0 +
chr1 3033216 3044416 ENSMUSG00000064842.1/U6 0 -
Samtools counts the read only once:
samtools view -c -q 1 -F 4 -L matrix_small_f.bed super_short.bam
1
samtools view -c -q 1 -F 4 -L matrix_small_f.bed super_short.bam
HWI-ST227:372:C3UVCACXX:3:1212:16462:69280 0 chr1 3044215 255 50M * 0 0 TCCAAGATTGGTGCCGAGCCCTATTGGCCCAAGTTAGAAGTAGACATCTG CCCFFFFFHHHHHJJJJJIJJJJJIGGJJJJJJHHIIJHIBFHIJJJIIG XA:i:0 MD:Z:50 NM:i:0
If I split my bed file into two separate files containing the first and the second regions, samtools shows the same read for each file.