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most of the bisulfite sequencing mapper support SAM output format. In order to support downstream analysis, bsmapper will be support SAM format, too.
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Running `$ picard ValidateSamFile INPUT=xxxxx-ready.bam` (bam file produced by bcbio-nextgen) gives the error listed below. Is this due to bam files being merged? Any potential problems from this, rea…
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What do people think about a name for this mapper? The defining features are that it makes use of a two-letter alphabet and is therefore optimized for bisulfite treated reads, and makes use of a hash…
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Section 2.4 of the MethPipe manual states that "[s]ince symmetric methylation is the common case for CpG methylation, we have _designed all of our analysis tools based on symmetric CpG sites_, which m…
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Using the current 1.878 picard CollectGcBiasMetrics (picard.jar CollectGcBiasMetrics) I get the error reported below. This occurs with Java 1.6.0 and Java 1.8. When I use an older picard (1.78, dire…
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Is it possible to extract read identifier(s) associated with a particular pattern by having it displayed (and if possible saved or output somewhere) when one mouse over a particular pattern in the plo…
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sr320 updated
9 years ago
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`CollectGcBiasMetrics` throws `java.lang.IndexOutOfBoundsException` and I don't see why.
At first, I thought this might be due difference in java versions. The same command worked on one system with …
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sr320 updated
9 years ago
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See: http://sourceforge.net/p/samtools/mailman/message/33435794/
> So this may be more challenging than initially thought. I am working of f the following branch: https://github.com/broadinstitute/pi…