User: ahaswer

gravatar for ahaswer
ahaswer70
Reputation:
70
Status:
Trusted
Location:
Czech Republic
Last seen:
13 minutes ago
Joined:
5 years, 2 months ago
Email:
k****************@gmail.com

about me

Posts by ahaswer

<prev • 18 results • page 1 of 2 • next >
1
vote
2
answers
300
views
2
answers
Comment: C: Removing duplicated mutations from a txt
... Use bash uniq: sort -r file.txt | uniq > output.txt ...
written 5 days ago by ahaswer70
0
votes
1
answer
162
views
1
answers
Comment: C: extra gene ids in gene count matrix than in gtf file
... In fact your gtf file (Oryza_sativa.IRGSP-1.0.37.gtf) does contain "EPlOSAG" ids, (short for Ensembl Plants Oryza sativa genes), check: grep -i "eplosag" Oryza_sativa.IRGSP-1.0.37.gtf | head However they are fine identifiers of genes/transcripts. The newest gtf file of O. sativa (1.0.42) conta ...
written 11 days ago by ahaswer70
0
votes
1
answer
162
views
1
answers
Comment: C: extra gene ids in gene count matrix than in gtf file
... I don't recall any annotation id starting with "EPIOSAG". Can you show command that you used while creating merged gtf file with stringtie? Maybe you used name prefix for output transcripts (the -l flag). Also keep in mind that stringtie provides two count files: gene counts and transcript counts. A ...
written 12 days ago by ahaswer70
0
votes
1
answer
162
views
1
answers
Answer: A: extra gene ids in gene count matrix than in gtf file
... Do the ids start with "MSTRG"? You will always get additional ids while using annotation. The reason for that is that the annotation file never contains 100% of complete genes and isoforms. Therefore every transcript which is not included in annotation will be assigned with 'MSTRG' identifier. If yo ...
written 13 days ago by ahaswer70
0
votes
2
answers
146
views
2
answers
Comment: C: Sorting out CD HiT output
... Replace [1-9] with [0-9] in awk command provided by 5heikki. ...
written 23 days ago by ahaswer70
0
votes
2
answers
146
views
2
answers
Comment: C: Sorting out CD HiT output
... Can you provide the file in the code window? I'm not sure about your field separators (specify them). It seems like single whitespaces. ...
written 23 days ago by ahaswer70
0
votes
2
answers
146
views
2
answers
Answer: A: Sorting out CD HiT output
... Assuming that the first line of file is the comment line you can simply use awk command: awk -F'[ _]' 'NF>0 && NR>1 {print $1" "$4}' cdhit.txt | sort | uniq -c | awk '{print $2, $3, $1}' > counts.txt I'm not sure if your file contains any blank lines. Running the command you w ...
written 23 days ago by ahaswer70
1
vote
3
answers
242
views
3
answers
Comment: C: cDNA to protein conversion
... So you just have list of changes which looks like this? c.562 C>A t.712 C>G etc. Do you have FASTA sequence of the unmutated gene? ...
written 24 days ago by ahaswer70
0
votes
1
answer
175
views
1
answers
Comment: C: RNA-seq Differential Gene Analysis
... That's for sure. I was just bit surprised to hear that one should never apply FC threshold. ...
written 24 days ago by ahaswer70
0
votes
1
answer
175
views
1
answers
Comment: C: RNA-seq Differential Gene Analysis
... Can you elaborate on that? ...
written 24 days ago by ahaswer70

Latest awards to ahaswer

Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Creating Count Matrix
Popular Question 22 months ago, created a question with more than 1,000 views. For Searching Annotation For Microarray Gene Expression Data.
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Mapping transcripts on reference genome

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1105 users visited in the last hour