User: anoo

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anoo0
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Posts by anoo

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Comment: C: Issues running RNAseqc on my bam file
... Hello, I am working on RNASeQC and came across the same error. RNA-SeQC v1.1.9 06/26/16 Creating rRNA Interval List based on given GTF annotations Retriving contig names from reference contig names in reference: 639 Loading GTF for Read Counting Converting to refGene Transcript objects to ...
written 6 weeks ago by anoo0
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Comment: A: RNA-SeQC v1.1.8 transcript_id attribute was not found
... Hello, Did you solve the error given above? I am also facing the same error with RNA-SeQC. Any help is appreciated. ...
written 7 weeks ago by anoo0
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Comment: C: RPKM with bowtie output
... I used the same commands given in the manual, with the BAM files I have, `software/RSEM-1.2.25/rsem-calculate-expression -p 8 --paired-end \ --bam \ --estimate-rspd \ --append-names \ --output-genome-bam \ exp/LPS_6h.bam \ ref/mouse_ref exp/LPS_6h` Error: Warning: Th ...
written 9 weeks ago by anoo0
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Comment: C: RPKM with bowtie output
... Hello, Can you please provide the steps used for calculating expression using RSEM, after building the reference. The script is throwing errors. ...
written 9 weeks ago by anoo0
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Comment: C: RSEM Error - rsem-calculate-expression
... Hello Adam, thanks for your response. The organism I am working on is Rat. When i tried building the index using the following command, it worked. rsem-prepare-reference --gtf /home/user/data/genome/Rattus_6/Rattus_norvegicus.Rnor_6.0.98.gtf \ --bowtie2 --bowtie2-path /home/user/data/bowtie2-2.3. ...
written 9 weeks ago by anoo0
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RSEM Error - rsem-calculate-expression
... Hello, I tried to calculate the expression using RSEM rsem-calculate-expression and came across few errors. The below given are the errors: Cannot open /.../.../../RSEM/.grp! It may not exist. /....sorted.bam 3 -tag XM" failed! Plase check if you provide correct parameters/options for ...
rsem-calculate-expression fpkm rsem rna-seq written 9 weeks ago by anoo0 • updated 9 weeks ago by h.mon29k

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