rcorbett
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Recent activity by rcorbett Sort by recent activity-
OK. I think we're making some progress here. I am starting with a refseq .gtf file where the annotation for my rRNA looks like this: chrUn_GL000220v1 BestRefSeq transcript 105424 118780 . + . ge...
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Many thanks for your help Genevieve-Brandt-she-her. It is more that I am confused by the output. I am not expecting a high UTR amount as my data are almost exclusively ribosomal and 45S, to my kno...
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OK. I uploaded a file called filterSamReads_output_format.tar.gz I was surprised to not be asked for a password at the following address, so it might be worth checking if the file is in fact on you...
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Thank you. I tried the same command with 4.1.9.0 and got the same errors. I will create a bug report.
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Good afternoon. gatk ValidateSamFile -I passed.bam -M SUMMARY Summary output: ## HISTOGRAM java.lang.StringError Type CountERROR:MISMATCH_FLAG_MATE_NEG_STRAND 14964150WARNING:ADJACENT_INDEL_IN_CI...
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Hi Genevieve-Brandt-she-her, For 1. above:gatk PrintReads -I stdout.bam -O tmp.tmp --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true'Using GATK jar /gsc/software/linux-x86_64-centos6/gatk-4....
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Thanks Genevieve, If I looks through the file I don't see anything human readable. Similarly, if I try strings stdout.bam I don't see anything of note. Just a little more information on the above...
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Hi again, we tried the same command on a BWA 0.7.6a mem aligned bam and ran in to the same issue.