multiple mapping with outFilterMultimapNmax 1

[K. Zhang]

Hi,

I was trying to filter out multiple mappings by using -- outFilterMultimapNmax 1, but there were still multiple mapped reads in the output. Does anyone have an idea why this happens?

options used: "--outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBan Singleend --limitBAMsortRAM 20000000000 --outFilterMismatchNmax 3, outFilterMultimapNmax 1"

and an example of the output:

HISEQ2:398:C8Y8YACXX:1:1210:4689:76627_GGGTTA   272     1       10108   0       13S33M  *       0       0       TGTGTATAAGAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAA  IJJJIJJJJJJJJJJJJIIIIIJHGGGCIIFGC<IIHGE<HIHHFC  NH:i:5  HI:i:3  AS:i:30 nM:i:1

HISEQ2:398:C8Y8YACXX:1:1216:20680:42261_GGGAAA  272     1       10108   0       13S33M  *       0       0       TGTGTATAAGAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAA  @HGIIIIIIIIGGIHFGHGBFFGGHBC?GHFB@;IIHBE:IHFCA<  NH:i:5  HI:i:3  AS:i:30 nM:i:1

HISEQ2:398:C8Y8YACXX:1:1315:6081:60599_GGGATA   272     1       10108   0       13S33M  *       0       0       TGTGTATAAGAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAA  GDCBGHGEGGGBGGIGEGGHFDCFDF:3FDFFGCDDFFBHGF?FF<  NH:i:5  HI:i:3  AS:i:30 nM:i:1

HISEQ2:398:C8Y8YACXX:1:1315:7535:65134_GGGTAA   272     1       10108   1       7S39M   *       0       0       TAAGAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA  IJJJIGJJJJJIICGGGJIHFDCHGGG?IJIJIGIJHGGGIGFHDA  NH:i:3  HI:i:3  AS:i:36 nM:i:1

HISEQ2:398:C8Y8YACXX:1:2105:12629:20146_GGGTTA  272     1       10108   1       7S39M   *       0       0       TAAGAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA  @DAHFFBADD@HEF@FB@B::3GGC?GE@FEDFFHFC:C<@EAFC<  NH:i:3  HI:i:3  AS:i:36 nM:i:1

HISEQ2:398:C8Y8YACXX:1:2209:13834:65321_GGGTTA  272     1       10108   1       7S39M   *       0       0       TAAGAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA  GJIJIJIJJJJJIHGDJGGHGDJIGCE;IGHGGEJHFEEEJIHHHD  NH:i:3  HI:i:3  AS:i:36 nM:i:1

HISEQ2:398:C8Y8YACXX:1:2216:20739:51124_GGGTTA  272     1       10108   0       13S33M  *       0       0       TGTGTATAAGAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAA  FFBGIIGGIIIGHIGAHG?=GDCFFEHGDEGGIHGGFCECGGCBA<  NH:i:5  HI:i:3  AS:i:30 nM:i:1

HISEQ2:398:C8Y8YACXX:1:2216:14820:82396_GGGTTA  272     1       10108   0       13S33M  *       0       0       TGTGTATAAGAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAA  ;@<F>FFF9FF9FEFCCD<E@FDDB?@?83A2A2>FA:A<@G?;A<  NH:i:5  HI:i:3  AS:i:30 nM:i:1

HISEQ2:398:C8Y8YACXX:1:2310:3325:48057_GGGCAA   272     1       10108   0       13S33M  *       0       0       TGTGTATAAGAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAA  GIIIGIIGIGIHEIGIIIGCIHEFD9G;FE?A<<IHFG@DGFDDDA  NH:i:5  HI:i:3  AS:i:30 nM:i:1

HISEQ2:398:C8Y8YACXX:1:1210:4689:76627_GGGTTA   16      1       180747  0       14S32M  *       0       0       TGTGTATAAGAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAA  IJJJIJJJJJJJJJJJJIIIIIJHGGGCIIFGC<IIHGE<HIHHFC  NH:i:5  HI:i:1  AS:i:31 nM:i:0

HISEQ2:398:C8Y8YACXX:1:1216:20680:42261_GGGAAA  16      1       180747  0       14S32M  *       0       0       TGTGTATAAGAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAA  @HGIIIIIIIIGGIHFGHGBFFGGHBC?GHFB@;IIHBE:IHFCA<  NH:i:5  HI:i:1  AS:i:31 nM:i:0

HISEQ2:398:C8Y8YACXX:1:1315:6081:60599_GGGATA   16      1       180747  0       14S32M  *       0       0       TGTGTATAAGAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAA  GDCBGHGEGGGBGGIGEGGHFDCFDF:3FDFFGCDDFFBHGF?FF<  NH:i:5  HI:i:1  AS:i:31 nM:i:0

Thanks in advance for your help!

- Kaiyang

[Alexander Dobin]

Hi Kaiyang

it looks like you have --outFilterMismatchNmax 3, outFilterMultimapNmax 1 in the command line while you need

--outFilterMismatchNmax 3 --outFilterMultimapNmax 1

If you loook in the Log.out file, you can find your command line and parameters as read by STAR:

##### Command Line:

...

###### All USER parameters from Command Line:

...

Cheers

Alex