User: c.zijlstra

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c.zijlstra0
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Posts by c.zijlstra

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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 15 months ago by c.zijlstra0
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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 15 months ago by c.zijlstra0
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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 15 months ago by c.zijlstra0 • updated 15 months ago by Jennifer Hillman Jackson24k
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'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 16 months ago by c.zijlstra0 • updated 16 months ago by Jennifer Hillman Jackson24k
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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 16 months ago by c.zijlstra0
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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 16 months ago by c.zijlstra0 • updated 16 months ago by Jennifer Hillman Jackson24k
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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 2.1 years ago by c.zijlstra0

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