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Created 2015-10-24 16:10:33 | Updated | Tags: indelrealigner mrnaseq memory

Comments (3)

I have 2 samples of RNAseq with 10 million PE reads for each and read length of 81 bp. indelRealigner gave me this error

ERROR MESSAGE: There was a failure because you did not provide enough memory to run this program. See the -Xmx JVM argument to adjust the maximum heap size provided to Java

I increased the heap size to 78g. One sample was done successful but the 2nd sample are still giving the same error. I tried to use down sampling but still the same error

Here is my code:

java -Xmx78g -jar $GATK/GenomeAnalysisTK.jar \ -T IndelRealigner \ -R $gatk_ref \ -I $sample \ -targetIntervals gatk.intervals \ -nWayOut '.realigned.bam' \ -known $indels \ -model USE_SW \ -LOD 0.4 \ -dcov 1000

Any advice will be truly appreciated. Thank you

Created 2015-09-21 08:14:52 | Updated | Tags: strand-bias mrnaseq

Comments (2)


I was wondering if it makes sense to filter for strand bias as stated in the Best Practice RNAseq Variant Calling guide as most of todays RNAseq data is strand specific. I would actually expect high strand biases of variants and be suspicious about variants which do NOT show strand bias =) ...or did i get something wrong with the Fisher Strand values?

Thank you

Created 2013-10-24 11:31:46 | Updated 2013-10-24 11:38:15 | Tags: snp rnaseq snps mrnaseq

Comments (2)

Hi! I have worked some time on a mRNAseq set, single-end. Its a high quality set and lots of biological replicates (200+).

My question is, how could I best contribute to the methodology used for SNPs call in mRNAseq? What do we need tested to improve this method?