RSEM Users

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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 Ajay4

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

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

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

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

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 Padilla4

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 Peter3

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

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 Li3

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

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

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

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 Wang2

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 Li2

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 Wilson2

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

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

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

10/12/20

Hi everyone, I have a couple of questions regarding running EBSeq. First, is there a way to annotate

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Hi everyone, I have a couple of questions regarding running EBSeq. First, is there a way to annotate

10/12/20

afreed...@gmail.com, Peng2

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

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

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 Li5

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

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