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Marzie E. Rasekh
Sep 20
rsem-simulate-read does not produce any fastq files.
When I run simulate-read, I get the fasta file, sim.genes.results, and sim.isoforms.results but no
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rsem-simulate-read does not produce any fastq files.
When I run simulate-read, I get the fasta file, sim.genes.results, and sim.isoforms.results but no
Sep 20
Zhuyi Xue
, …
Abhishek Ajay
4
Mar 30
Bam file created, but no alignable.fq.
Hi! I am getting the same error. You mention that the error message suggests that it's a single
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Bam file created, but no alignable.fq.
Hi! I am getting the same error. You mention that the error message suggests that it's a single
Mar 30
Xunzhi Zhang
Feb 2
Calculate the TPM values after running Combat-seq
Hello, In the output of RSEM, there are "length" and "effective_length" columns
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Calculate the TPM values after running Combat-seq
Hello, In the output of RSEM, there are "length" and "effective_length" columns
Feb 2
Christopher Bryan
11/3/22
Error Using RSEM Prepare Reference
Command: rsem-prepare-reference --gtf index/gencode.v23lift37.annotation.gtf \ --star index/GRCh37.
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Error Using RSEM Prepare Reference
Command: rsem-prepare-reference --gtf index/gencode.v23lift37.annotation.gtf \ --star index/GRCh37.
11/3/22
Rashmi Kallath
10/31/22
rsem-calculate-credibility-intervals
Hi All, I am not sure why many questions remains unanswered here. Today I tried to run rsem
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rsem-calculate-credibility-intervals
Hi All, I am not sure why many questions remains unanswered here. Today I tried to run rsem
10/31/22
Rashmi Kallath
10/30/22
RSEM - sorting and error with calculate expression
Dear RSEM group, I am new to rnaseq. I am going through the tutorial https://ycl6.gitbook.io/guide-to
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RSEM - sorting and error with calculate expression
Dear RSEM group, I am new to rnaseq. I am going through the tutorial https://ycl6.gitbook.io/guide-to
10/30/22
Naveen prasath
10/18/22
rsem-calculate expression
#!/bin/bash GTF="/home/student/UCD1.2.99.gtf" FNA="/home/student/UCD1.2.dna.toplevel.
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rsem-calculate expression
#!/bin/bash GTF="/home/student/UCD1.2.99.gtf" FNA="/home/student/UCD1.2.dna.toplevel.
10/18/22
INMEGEN SALAZAR
, …
David Padilla
4
7/24/22
Fail to create folder /dir.temp.
You may be trying to create the .temp folder in a folder that does not exist. El jueves, 20 de julio
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Fail to create folder /dir.temp.
You may be trying to create the .temp folder in a folder that does not exist. El jueves, 20 de julio
7/24/22
Yvonne Zhao
,
Ruban Rex Peter
3
6/22/22
rsem-calculate-expression error message
Yes, I did! It worked out when I replace the RSEM package included in the tutorial package with an
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rsem-calculate-expression error message
Yes, I did! It worked out when I replace the RSEM package included in the tutorial package with an
6/22/22
Hope Kirby
2/8/22
RSEM ref genome problems
Hi! So I am trying to do basic RNAseq using a reference genome I created witth RSEM Code for creating
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RSEM ref genome problems
Hi! So I am trying to do basic RNAseq using a reference genome I created witth RSEM Code for creating
2/8/22
Fleur Peters
,
Bo Li
3
9/21/21
rsem-calculate-expression running time endless but also no error
Hi Bo, Thanks for your reply. Indeed separately doing the alignment and then using the aligned.
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rsem-calculate-expression running time endless but also no error
Hi Bo, Thanks for your reply. Indeed separately doing the alignment and then using the aligned.
9/21/21
Anindyajit Banerjee
8/18/21
rsem-prepare-reference --allele-to-gene-map <file> (file information required)
--allele-to-gene-map <file> Use information from <file> to provide gene_id and
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rsem-prepare-reference --allele-to-gene-map <file> (file information required)
--allele-to-gene-map <file> Use information from <file> to provide gene_id and
8/18/21
Jared Rozowsky
8/9/21
rsem-calculate-expression running time
Hi, Hoping someone can help. It seems like it is taking a long time to run calculate-expression on my
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rsem-calculate-expression running time
Hi, Hoping someone can help. It seems like it is taking a long time to run calculate-expression on my
8/9/21
Alexis Brown
7/5/21
rsem-calculate-credibility-intervals failing
Hello, I have been trying to use rsem to quantify expression and calculate credibility intervals on
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rsem-calculate-credibility-intervals failing
Hello, I have been trying to use rsem to quantify expression and calculate credibility intervals on
7/5/21
Crystal Gowda
7/3/21
rsem-calculate-expression error
I have prepared reference using the command: rsem-prepare-reference -p 5 --bowtie2 cd_hit_est.fasta
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rsem-calculate-expression error
I have prepared reference using the command: rsem-prepare-reference -p 5 --bowtie2 cd_hit_est.fasta
7/3/21
JiYeon Han
,
Yu Wang
2
6/8/21
inconsistent read length!
Hi, all Read A00632:98:HC27MDRXY:1:2102:2799:1047 has alignments with inconsistent read lengths! Did
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inconsistent read length!
Hi, all Read A00632:98:HC27MDRXY:1:2102:2799:1047 has alignments with inconsistent read lengths! Did
6/8/21
afreed...@gmail.com
,
Bo Li
2
5/28/21
rsem-prepare-reference errors with augustus gff
Hi Adam, Happy to address this issue. Can you send me the augustus gff3 file so that I can repeat
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rsem-prepare-reference errors with augustus gff
Hi Adam, Happy to address this issue. Can you send me the augustus gff3 file so that I can repeat
5/28/21
Pamela DIFL4259
5/21/21
Cannot read alignments from .dat file!
Hello, I was running RSEM on files from Pseudomonas aeruginosa and this error came up. I don't
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Cannot read alignments from .dat file!
Hello, I was running RSEM on files from Pseudomonas aeruginosa and this error came up. I don't
5/21/21
samantha_...@brown.edu
,
Khadija Wilson
2
5/5/21
rsem-run-em FAILED (-p / threads error) v1.3.0
Hi, were you able to fix this? On Saturday, May 26, 2018 at 12:07:31 PM UTC-4 samantha_...@brown.edu
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rsem-run-em FAILED (-p / threads error) v1.3.0
Hi, were you able to fix this? On Saturday, May 26, 2018 at 12:07:31 PM UTC-4 samantha_...@brown.edu
5/5/21
Khadija Wilson
5/3/21
rsem-run-em failed!
Hi, I am trying to perform rsem-calculate-expression using STAR aligned .bam files - I generated a
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rsem-run-em failed!
Hi, I am trying to perform rsem-calculate-expression using STAR aligned .bam files - I generated a
5/3/21
Abhilash KANNAN
1/22/21
RSEM-calculate-expression non determinsitic?
Dear RSEM community, I am having an issue of non-deterministic counts of alt/ref alleles in the RNA-
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RSEM-calculate-expression non determinsitic?
Dear RSEM community, I am having an issue of non-deterministic counts of alt/ref alleles in the RNA-
1/22/21
Abhilash KANNAN
1/22/21
Question: The two mates do not align to a same transcript -- RSEM error
Hello RSEM Community, I am trying to to run rsem-calculate-expression using STAR to aligned reads.
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Question: The two mates do not align to a same transcript -- RSEM error
Hello RSEM Community, I am trying to to run rsem-calculate-expression using STAR to aligned reads.
1/22/21
Fernando J.
11/2/20
rsem-calculate-expresion returns "The SAM/BAM file declares less than one reference sequence!"
Hi! I am trying to replicate an experiment using RSEM to perform RNA analysis (https://www.nature.com
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rsem-calculate-expresion returns "The SAM/BAM file declares less than one reference sequence!"
Hi! I am trying to replicate an experiment using RSEM to perform RNA analysis (https://www.nature.com
11/2/20
Chuan Foo
10/12/20
EBSeq
Hi everyone, I have a couple of questions regarding running EBSeq. First, is there a way to annotate
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EBSeq
Hi everyone, I have a couple of questions regarding running EBSeq. First, is there a way to annotate
10/12/20
afreed...@gmail.com
,
Peng
2
9/23/20
--limitGenomeGenerateRAM not an available option for rsem-prepare-reference
Hi Adam, Thanks for bringing up this question. You can build STAR index outside of RSEM and run STAR
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--limitGenomeGenerateRAM not an available option for rsem-prepare-reference
Hi Adam, Thanks for bringing up this question. You can build STAR index outside of RSEM and run STAR
9/23/20
kallet
,
Peng
7
7/31/20
RSEM+STAR with modified GTF
keskiviikko 29. heinäkuuta 2020 14.34.52 UTC+3 kallet kirjoitti: Hi all RSEM users, I'm applying
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RSEM+STAR with modified GTF
keskiviikko 29. heinäkuuta 2020 14.34.52 UTC+3 kallet kirjoitti: Hi all RSEM users, I'm applying
7/31/20
Dekel Wainer
7/15/20
What are acceptable results in rsem-plot-model?
Hi all! I performed rsem-calculate-expression on 4 samples and received what seems to me low-quality
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What are acceptable results in rsem-plot-model?
Hi all! I performed rsem-calculate-expression on 4 samples and received what seems to me low-quality
7/15/20
Raj Sasidharan
,
Bo Li
5
6/18/20
Discrepancy in alignment stats between outputs from STAR and RSEM (.cnt file)
Thank you Bo. I think it would be useful for RSEM to report aligned, unaligned reads wrt total reads
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Discrepancy in alignment stats between outputs from STAR and RSEM (.cnt file)
Thank you Bo. I think it would be useful for RSEM to report aligned, unaligned reads wrt total reads
6/18/20
Andrei Rozanski
5/25/20
QuantSeq 3' mRNA-Seq
Hello, I would like to clarify if I can use RSEM to calclulate expression of 3' seq data (https:/
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QuantSeq 3' mRNA-Seq
Hello, I would like to clarify if I can use RSEM to calclulate expression of 3' seq data (https:/
5/25/20
Michelle Wedemeyer
5/11/20
"Two mates aligned to two different transcripts!" OR "One alignment line has SEQ field as *" rsem-tbam2gbam failed!
Hello, Apologies if this has been posted somewhere that my very novice search missed but I have been
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"Two mates aligned to two different transcripts!" OR "One alignment line has SEQ field as *" rsem-tbam2gbam failed!
Hello, Apologies if this has been posted somewhere that my very novice search missed but I have been
5/11/20