User: y.hoogstrate

gravatar for y.hoogstrate
y.hoogstrate440
Reputation:
440
Status:
Trusted
Location:
Netherlands
Last seen:
1 month ago
Joined:
3 years, 3 months ago
Email:
y***********@gmail.com

Posts by y.hoogstrate

<prev • 74 results • page 1 of 8 • next >
0
votes
4
answers
339
views
4
answers
Comment: C: User Tool Does Not Initialize
... Ooops, those comments should be replaced with CDATA tags (blame me!): ``` $output/file.txt ]]> ``` "After I fixed that, the program doesn't hang anymore, but it just doesn't start now." Does the whole Galaxy wrapper not load, or does the command not get executed? *This program is a wrapper fo ...
written 8 weeks ago by y.hoogstrate440
1
vote
1
answer
93
views
1
answers
Answer: A: Regarding splitter or merging the paired end sequencing file
... This can be a frustrating problem as the order in the file is often used to link R1 and R2 files rather than the names of the sequencing reads. The tools Sickle (low quality trimming only) and Trimmomatic are aware of this and put the reads of which the mate has been discarded in a separate file. Th ...
written 9 weeks ago by y.hoogstrate440
0
votes
4
answers
339
views
4
answers
Comment: C: User Tool Does Not Initialize
... Could you do something like: ``` ``` and see if this hangs? ...
written 9 weeks ago by y.hoogstrate440
1
vote
1
answer
81
views
1
answers
Comment: C: HELP! My HT seq table counts are in zero
... Devon's thought was right I suppose. Your BAM/SAM file was aligned to sequences named 'NW_003302556.1' etc while your GTF file contains sequences named 'supercont1.1'. These do not correspond causing HTSeq to not find reads aligned to 'supercont1.1'. ...
written 12 weeks ago by y.hoogstrate440
2
votes
2
answers
116
views
2
answers
Answer: A: Data managers tool: the content of data table disappear after restart Galaxy
... Galaxy makes clones of these loc files for each revision of each installed tool and does not write content always to the loc file directly in ./tool-data. In older versions of Galaxy it was possible to find all corresponding loc files via the web interface but this has disappeared some time ago. Any ...
written 3 months ago by y.hoogstrate440
0
votes
2
answers
116
views
2
answers
Answer: A: Data managers tool: the content of data table disappear after restart Galaxy
... This does not sound like normal Galaxy behaviour. Did you test this in planemo or in a Galaxy instance? Galaxy usually writes to flat LOC files and as far as I know there is no mechanism that automatically reverts or resets. Is the name of the loc file not used by others tools maybe? Does your file ...
written 3 months ago by y.hoogstrate440
0
votes
3
answers
120
views
3
answers
Answer: A: BAM files fail to be recognized
... Those are SAM files, not BAM files. Can you convert (revert?) them with 'SAM-to-BAM convert SAM to BAM' and see if that works out for you? ...
written 3 months ago by y.hoogstrate440
0
votes
3
answers
235
views
3
answers
Answer: A: STAR in multiple threads faces issues in opening genome file
... how much memory do you have in that machine? The Galaxy wrapper has set `--genomeLoad NoSharedMemory` (default STAR option). The consequence is that running two jobs in parallel, makes two copies of the reference genome (~30gb) in the RAM. Could this have anything to do with it? ...
written 5 months ago by y.hoogstrate440
1
vote
3
answers
235
views
3
answers
Answer: A: STAR in multiple threads faces issues in opening genome file
... Do you use references genomes from history or from Galaxy's cache and are you running STAR on identical or Different references? ...
written 5 months ago by y.hoogstrate440
0
votes
4
answers
339
views
4
answers
Comment: C: User Tool Does Not Initialize
... This is where work starts to become fun ;) ...
written 6 months ago by y.hoogstrate440

Latest awards to y.hoogstrate

Scholar 9 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Scholar 10 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Scholar 10 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Scholar 10 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Supporter 15 months ago, voted at least 25 times.
Scholar 18 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Scholar 18 months ago, created an answer that has been accepted. For A: Is HISAT2 working in GALAXY?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Is HISAT2 working in GALAXY?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Making PNG figures from plots in R from toolshed (without X11)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 123 users visited in the last hour