User: lukacdm

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lukacdm0
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United States
Last seen:
5 months ago
Joined:
3 years, 11 months ago
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l******@njms.rutgers.edu

Posts by lukacdm

<prev • 16 results • page 1 of 2 • next >
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Bowtie 2 An error occurred setting the metadata for this dataset
... Hi: the message "An error occurred setting the metadata for this dataset" is appearing in all of my Bowtie2 runs today, regardless of server. The auto detect button is not correcting the error. Thanks. ...
bowtie metadata written 5 months ago by lukacdm0 • updated 5 months ago by Jennifer Hillman Jackson24k
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Filter BAM app in Bam Tools
... I'm trying to eliminate inserts larger than 500 bp in a Bam file generated by Bowtie2 using the Filter BAM app in BAMTools (filter on insert size <=500). The largest read reported for the input Bam file is 81267 bp; hence, I want to delete all reads between 501 and 81267 bp. When I use the Picar ...
bam filter insert size written 23 months ago by lukacdm0 • updated 23 months ago by Jennifer Hillman Jackson24k
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Galaxy app to retrieve selected raw reads
... There are many previous threads regarding how to retrieve selected raw reads from fastq files offline; does anyone know of a public galaxy instance with a tool that can return a set of raw reads using a query of post-filtered, post-mapped reads? ...
filter retrieve tool fastq written 24 months ago by lukacdm0 • updated 24 months ago by Jennifer Hillman Jackson24k
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Nearest Neighbor analysis
... Does anyone know of a public galaxy instance that can run a nearest neighbor analysis to compare ChIP-Seq peak locations with user-inputted genomic features like TSSs and other DNA motifs?  Thanks in advance. ...
nearest neighbor written 2.6 years ago by lukacdm0 • updated 2.5 years ago by Bjoern Gruening5.0k
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Filter Wig file
... I would like to filter a wig file from a ChIPSeq Peak calling program by its control ChIPSeq Peak wig file, i.e., to output only peaks that have greater height in the ChIP antibody from the control antibody, or from the input file.  I would like the output to be wig or bigwig for IGV visulatization. ...
chip seq wig written 3.1 years ago by lukacdm0 • updated 3.1 years ago by Jennifer Hillman Jackson24k
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My queue is frozen
... Hi, can someone from the Galaxy Admin team check my account?  My queue has been frozen for 3 days; I executed a number of different tools, and re-executed a previous analysis that previously worked.  All of them are stuck in grey with no activity.   Thanks.  ...
queue written 3.3 years ago by lukacdm0 • updated 3.3 years ago by Jennifer Hillman Jackson24k
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Bowtie2 not running
... Hello, I have 4 Bowtie2 analyses that I executed about 18 hours ago that are still grey and queued.  I had a slightly older analysis that did complete and returned data.  To test Bowtie2, I re-executed the completed analysis, and it is also hung up in queue.  Can someone check whether Bowtie2 is wor ...
bowtie2 written 3.3 years ago by lukacdm0
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Answer: A: Paired-end insert size upper limit
... Thanks so much.  I usually use other galaxy instances that have appropriate Peak Calling programs. ...
written 3.3 years ago by lukacdm0
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Answer: A: Paired-end insert size upper limit
... Thanks, Jennifer.  Will peak calling programs also ignore the long inserts? ...
written 3.3 years ago by lukacdm0
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Paired-end insert size upper limit
... I am mapping paired-end reads using Bowtie2 and setting "maximum insert size for valid paired-end alignments" to 500 bases. However, when I calculate the insert sizes of the resulting bam files using Picard Insert Size Metrics I frequently see one or two inserts per file that exceed 20000 bases.  Is ...
bowtie2 picard insert size metrics written 3.3 years ago by lukacdm0

Latest awards to lukacdm

Popular Question 23 months ago, created a question with more than 1,000 views. For Splitting Biased Paired End FASTQ data
Popular Question 23 months ago, created a question with more than 1,000 views. For Ftp to History file upload
Popular Question 23 months ago, created a question with more than 1,000 views. For Paired-end insert size upper limit

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