User: jcm136

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jcm1360
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Posts by jcm136

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Comment: C: RNAseqC: WARNING: Transcript has no coverage
... Thanks for the reply. I have suspected 18S contamination. Unfortunately the gtf I am using is not annotated for 18S, although retrieving the Rhesus 18S sequence, BLATing it to find genomic coordindates, and then going to the location in IGV doesn't seem to yield any reads mapping to putative 18S s ...
written 3.7 years ago by jcm1360
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Comment: C: RNAseqC: WARNING: Transcript has no coverage
... Thank you. Pardon my naivety but if I can get the rDNA repeat sequence from Rhesus, how might I align an entire .fastq sample to it. ...
written 3.7 years ago by jcm1360
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Comment: C: RNAseqC: WARNING: Transcript has no coverage
... INFO 2016-11-01 15:31:26 SamFileValidator Validated Read 10,000,000 records. Elapsed time: 00:00:31s. Time for last 10,000,000: 31s. Last read position: chr03:117,226,161 INFO 2016-11-01 15:31:56 SamFileValidator Validated Read 20,000,000 records. Elapsed time: 00:01:01s. Time for last ...
written 3.7 years ago by jcm1360
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Comment: C: RNAseqC: WARNING: Transcript has no coverage
... OK...thank you so much for the reply. What I'm actually interested in is where the intronic or non-genic reads are mapping to. The reason being, although my alignment stats were good (~90% reads mapped with STAR), performing read counts on the .bam file with HT-seq count yielded a high number of r ...
written 3.7 years ago by jcm1360 • updated 3.7 years ago by Devon Ryan96k
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Comment: C: RNAseqC: WARNING: Transcript has no coverage
... For what it's worth, I'm getting the following ERRORs in the output log when running the GATK depth of coverage analysis: Running GATK Depth of Coverage Analysis .... Arguments: -T DepthOfCoverage -R ref_input/MacaM_Rhesus_Genome_v7.fasta -I bam_input/JB37_sorted_ReadGroup.bam -o .//JB37_so ...
written 3.7 years ago by jcm1360 • updated 3.7 years ago by Devon Ryan96k
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RNAseqC: WARNING: Transcript has no coverage
... Hello, I am working with a paired-end data set of rhesus macaque reads aligned with STAR against a current rhesus .fasta reference and .gtf annotation. I am interested in doing some quality control measures on my .bam file with **RNAseqC** to determine numbers of reads that map to non-genic, exoni ...
software error rna-seq written 3.7 years ago by jcm1360

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