User: c.zijlstra

gravatar for c.zijlstra
c.zijlstra0
Reputation:
0
Status:
New User
Location:
Last seen:
3 weeks, 6 days ago
Joined:
2 years, 10 months ago
Email:
c*********@uu.nl

Posts by c.zijlstra

<prev • 8 results • page 1 of 1 • next >
0
votes
1
answer
49
views
1
answer
how to sort reads by read length
... I would like to sort reads in a bam file by read length. Which tool on the galaxy website can i use? ...
bam galaxy sam sort written 28 days ago by c.zijlstra0 • updated 27 days ago by Jennifer Hillman Jackson25k
0
votes
1
answer
636
views
1
answers
Comment: C: sort reads by start position
... Hi Jennifer, I finally managed to do the filtering and sorting I wanted to do by using the tool ‘Filter data on any column..’. So Thanks again for your advice! Carla From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: dinsdag 1 november 2016 19:22 To: Zijlstra ...
written 2.0 years ago by c.zijlstra0
0
votes
1
answer
636
views
1
answers
Comment: C: sort reads by start position
... Thanks Jennifer! I tried the Group tool as you suggested but then I only find the number of reads per chromosome (not per gene) that starts exactly at the beginning of the regions defined in column 2. I would also like to sort reads that start at positions more towards 3’end of region of interest. ...
written 2.0 years ago by c.zijlstra0
0
votes
1
answer
636
views
1
answer
sort reads by start position
... I did RNA sequencing and many reads map to tRNA regions. Specific tRNAs are completely covered by all the reads that map to it, but many reads are not full-length tRNA. (So some reads start at 5'end while others start for example at base 20) To find out to which part of the tRNA reads correspond, ...
rna-seq written 2.1 years ago by c.zijlstra0 • updated 2.0 years ago by Jennifer Hillman Jackson25k
0
votes
1
answer
1.1k
views
1
answer
'BEDcov' and 'compute depth and breadth'
... In galaxy I used boht the SAMtool bedcov and the bedtool 'Compute both depth and breath' to calculate the read depth in my samples. However, I get quite different numbers for depth with the two tools (depth in bedcov always higher), How can this be explained?? kind regards, carla ...
bam samtools coverage bed bedtools written 2.1 years ago by c.zijlstra0 • updated 2.1 years ago by Jennifer Hillman Jackson25k
0
votes
1
answer
701
views
1
answers
Comment: C: Bedtools coverage not accepting file b
... Hi Tim, I understand you are using the tool compute both depth and breadth of coverage. Can you explain to me whether the outtput of this tool represents number of nucleotides mapped to a region, or number of alignments? Kind regards, carla ...
written 2.1 years ago by c.zijlstra0
0
votes
1
answer
456
views
1
answer
what features are counted by 'compute both depth and breadth'?
... I used the bed tool Compute both depth and breadth of coverage', but it is not clear to me whether output lists number of nucleotides or number of alignments that overlap an interval. Can someone please explain this? Kind regards, carla ...
galaxy written 2.1 years ago by c.zijlstra0 • updated 2.1 years ago by Jennifer Hillman Jackson25k
0
votes
0
answers
935
views
0
answers
uploading bam file
... I am trying to upload a bam file that was generated by rna-star (using Illumina1.9 sequencing data), but I get the following error: Has anyone a suggestion how to solve this problem??   Kind regards, Carla Zijlstra (c.zijlstra@uu.nl) ...
software error written 2.8 years ago by c.zijlstra0

Latest awards to c.zijlstra

Popular Question 23 months ago, created a question with more than 1,000 views. For 'BEDcov' and 'compute depth and breadth'

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 170 users visited in the last hour