User: Biocode_user

gravatar for Biocode_user
Biocode_user20
Reputation:
20
Status:
New User
Location:
Sweden
Last seen:
1 year, 6 months ago
Joined:
5 years, 1 month ago
Email:
l************@gmail.com

Posts by Biocode_user

<prev • 17 results • page 2 of 2 • next >
0
votes
1
answer
1.1k
views
1
answer
Piccard module(CollectRNASeqMetrics) error
... Hello, I am trying to get the mapping statistics from my bam file and i am mainly interested to look into how many reads map to cds, 5' and 3' UTR's. I a trying to use CollectRNASeqMetrics and i get the following error I used gtfToGenePred to convert my gtf file to refFlat file. and my refFlat loo ...
software error rna-seq written 4.0 years ago by Biocode_user20 • updated 3.6 years ago by cjsifuen0
0
votes
2
answers
5.6k
views
2
answers
Comment: A: Picard CollectRnaSeqMetrics error
... Hello, I am getting same error and could anyone please help me. I used gtfToGenePred to convert my gtf file to refFlat file. and my refFlat looks like Ec-00_000010.1 chr_00 - 149 6731 149 6731 10 149,897,1535,2091,2535,3474,4006,4702,6245,6709, 428,1100,1674,2 ...
written 4.0 years ago by Biocode_user20 • updated 18 days ago by RamRS25k
0
votes
2
answers
1.4k
views
2
answers
Comment: C: How to get an estimate the reads mapping to different regions of the genome and
... I have not worked much with R before. And it's not just about plotting. But I would like to know from scratch what should be done with the bam alignment file to get how the reads are mapped to different regions. I have no idea of how to get the read counts at different regions? ...
written 4.0 years ago by Biocode_user20 • updated 24 days ago by RamRS25k
0
votes
2
answers
1.4k
views
2
answers
How to get an estimate the reads mapping to different regions of the genome and plot to get the peak
... How can I get a density plot to get an idea of reads mapping to different regions of the genome. I see that only 40% of the reads maps to CDS and around 60% mapping to UTR's or some other non-coding RNA. I have generated a bam file after mapping the reads to genome. I could like to visualize this b ...
assembly rna-seq density plot written 4.0 years ago by Biocode_user20 • updated 4.0 years ago by Sukhdeep Singh10.0k
2
votes
1
answer
4.3k
views
1
answer
Error while mapping reads to assembly using bowtie
... I am trying to map assembly back to the reads using bowtie. But with one of the libraries, i get an error Error: Warning: skipping mate #2 of read 'DHKW5DQ1:246:C1D7AACXX:4:1101:7855DDDDDDDDDD@BCEEDDDDDDD5AGAAGAAGTCDACADECCDTGGGCGCC' because length (0) <= # seed mismatches (0) Warning: skipping ...
assembly rna-seq written 4.3 years ago by Biocode_user20 • updated 4.3 years ago by Antonio R. Franco4.3k
2
votes
1
answer
1.9k
views
1
answer
bash script to run clustalw and fetching sequences
... Hello, I'm trying to run a bash script. I need to execute on all the files in the folder. Here i'm posting the script  #!/bin/bash module bash load clustalw pal2nal exonerate file_path="/dirname/" source=`pwd` dir=`mktemp -d` && cd $dir for file in file_path;do echo "processsing "$file" file ...
software error written 5.0 years ago by Biocode_user20
0
votes
0
answers
1.5k
views
0
answers
Trouble in running Baseml
... Hello, I'm trying to do a nucleotide substitution analysis using a very simple model like Jukes and Cantor. I have a set of transcripts assembly and based on expression I have chosen the representative component of each  and did a reciprocal blastn on the  nucleotide sequences which is been jotted d ...
paml rna-seq written 5.1 years ago by Biocode_user20

Latest awards to Biocode_user

Popular Question 24 months ago, created a question with more than 1,000 views. For Trouble in running Baseml
Popular Question 2.2 years ago, created a question with more than 1,000 views. For bash script to run clustalw and fetching sequences
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Error while mapping reads to assembly using bowtie

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1043 users visited in the last hour