Files referred to in the last post by @Sajna are once again available at the same link.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
As per the RNASeq version 2 pipeline in the link below, I have been able to obtain outputs till step 11, i.e the transcriptome_alignments_filtered.bam output. Next step is to run rsem.
I ran RSEM using the following command : /opt/rsem-1.1.13/rsem-calculate-expression --paired-end --bam --estimate-rspd -p 8 transcriptome_alignments_filtered.bam /home/group_sh/TCGA+SRA_datamergerquantification_RNASeqV2/RSEM_ref_from_TCGA_webshare/hg19_M_rCRS_ref ERR519523.rsem > rsem.log_2 > rsem.log
I get this error in the log file :
rsem-parse-alignments failed! Please check if you provide correct parameters/options for the pipeline!
What is wrong? I donot understand. I am running exactly the same command!!!
Kindly help.
Comment
-
Have you done first part of step 4 in this document: https://tcga-data.nci.nih.gov/tcgafi...ESCRIPTION.txt
Comment
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
59 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
57 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
51 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
55 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment