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Phoebe Cunningham
9/19/23
Why does "reads genomic origin" sums to only a s fraction of total reads aligned?
Good morning, I am having trouble interpreting the results of my RNAseq qualimap. The results say
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Why does "reads genomic origin" sums to only a s fraction of total reads aligned?
Good morning, I am having trouble interpreting the results of my RNAseq qualimap. The results say
9/19/23
Wannes Dermauw
5/11/23
missing chromosome in annotation for RNAseq data
Hi I have the following output for RNAseq PE data: Analysis date: Thu May 11 09:34:46 CEST 2023 BAM
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missing chromosome in annotation for RNAseq data
Hi I have the following output for RNAseq PE data: Analysis date: Thu May 11 09:34:46 CEST 2023 BAM
5/11/23
Chelsea McLean
3/29/23
Difference in Exonic Mapping Rate - Qualimap vs RSeQC
Hi all, The Qualimap documentation says that "Exonic region includes 5'UTR, protein coding
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Difference in Exonic Mapping Rate - Qualimap vs RSeQC
Hi all, The Qualimap documentation says that "Exonic region includes 5'UTR, protein coding
3/29/23
Nina Hertoghs
3/23/23
The -pe,--paired setting results in big difference in exonic mapping
Hi all, We have some RNAseq data generated by a vendor, which resulted in lower than expected
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The -pe,--paired setting results in big difference in exonic mapping
Hi all, We have some RNAseq data generated by a vendor, which resulted in lower than expected
3/23/23
seth musker
2/23/23
bamqc not generating raw_data_qualimapReport subfolder
Hi, I'm using qualimap v2.2.1 on several samples. I've run bamqc on each of them and
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bamqc not generating raw_data_qualimapReport subfolder
Hi, I'm using qualimap v2.2.1 on several samples. I've run bamqc on each of them and
2/23/23
吳德倫(Soappp)
12/15/22
paired-end adapted mean coverage is only one-third of mean coverageData
Hello! I used `qualimap bam qc -ip -gff <bed>` to measure my bam and found that paired-end
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paired-end adapted mean coverage is only one-third of mean coverageData
Hello! I used `qualimap bam qc -ip -gff <bed>` to measure my bam and found that paired-end
12/15/22
Vlad Grigorjev
,
Konstantin Okonechnikov
4
12/9/22
Qualimap bamqc v2.2.2 Cannot invoke "org.bioinfo.ngs.qc.qualimap.beans.XYVector.getXVector()" because "this.data" is null
Great! Without feature file argument all read alignments are processed and for statistics/plots
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Qualimap bamqc v2.2.2 Cannot invoke "org.bioinfo.ngs.qc.qualimap.beans.XYVector.getXVector()" because "this.data" is null
Great! Without feature file argument all read alignments are processed and for statistics/plots
12/9/22
qianlong kang
,
Konstantin Okonechnikov
3
11/18/22
bamqc mapped reads 100%???
I see! Thank you very much!^_^ 在2022年11月15日星期二 UTC+8 21:15:24<Konstantin Okonechnikov> 写道: HI,
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bamqc mapped reads 100%???
I see! Thank you very much!^_^ 在2022年11月15日星期二 UTC+8 21:15:24<Konstantin Okonechnikov> 写道: HI,
11/18/22
Sonia Agrawal
, …
Konstantin Okonechnikov
8
11/10/22
QualiMap v 2.2.1 bamqc reporting incorrect total number of reads
Hi, most likely the issue that there are secondary alignments of the same read in the BAM file. The
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QualiMap v 2.2.1 bamqc reporting incorrect total number of reads
Hi, most likely the issue that there are secondary alignments of the same read in the BAM file. The
11/10/22
吳德倫(Soappp)
,
Konstantin Okonechnikov
3
11/1/22
estimated duplicated reads are more than total reads
Hi, Konstantin Like you saying, I found many supplementary alignments distributed in bam, and I used
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estimated duplicated reads are more than total reads
Hi, Konstantin Like you saying, I found many supplementary alignments distributed in bam, and I used
11/1/22
Amy Houseman
10/3/22
Is it possible to make coverage maps of specific genes?
Hello, I was wondering if it is possible to make coverage depth graphs of specific genes from the
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Is it possible to make coverage maps of specific genes?
Hello, I was wondering if it is possible to make coverage depth graphs of specific genes from the
10/3/22
Gautam Naishadham
,
Konstantin Okonechnikov
3
9/16/22
Add reporting on control sequences in RNA-seq
Great to hear your support for this! I am definitely interested in direct development, but I will
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Add reporting on control sequences in RNA-seq
Great to hear your support for this! I am definitely interested in direct development, but I will
9/16/22
Samuel Clamons
2
8/30/22
BAM file is empty
Never mind, a colleague figured it out—I was using the wrong output from STAR. On Monday, August 29,
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BAM file is empty
Never mind, a colleague figured it out—I was using the wrong output from STAR. On Monday, August 29,
8/30/22
Полина Казакова
,
Konstantin Okonechnikov
3
8/24/22
Unequal global summary in output files
Thanks for your answer! TXT files are the most easier for parsing and so I searched information about
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Unequal global summary in output files
Thanks for your answer! TXT files are the most easier for parsing and so I searched information about
8/24/22
Amy Houseman
,
Konstantin Okonechnikov
2
8/8/22
Combining qualimap results
Hi Amy, exactly for this purpose there MulitBAMQC mode in Qualitmap, it allows to merge results: http
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Combining qualimap results
Hi Amy, exactly for this purpose there MulitBAMQC mode in Qualitmap, it allows to merge results: http
8/8/22
Amy Houseman
,
Konstantin Okonechnikov
5
8/8/22
Some regions are not loaded warning
Hi Konstantinos, I reran my analysis and it turned out fine, I think some of my reads went missing
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Some regions are not loaded warning
Hi Konstantinos, I reran my analysis and it turned out fine, I think some of my reads went missing
8/8/22
Esther Kockelmans
,
Konstantin Okonechnikov
3
2/5/22
Bamqc more mapped reads than total reads in dataset?
Hi, Thanks for the quick respond. This is the command I used for the alignment (using minimap2): #
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Bamqc more mapped reads than total reads in dataset?
Hi, Thanks for the quick respond. This is the command I used for the alignment (using minimap2): #
2/5/22
Dragana Dudic
1/27/22
Zea_mays_v5.gtf Warning! Line with wrong attributes is skipped:
Hi, I have downloaded latest version of Zea mays gff3 from EnsemblPlants, converted it to gtf with
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Zea_mays_v5.gtf Warning! Line with wrong attributes is skipped:
Hi, I have downloaded latest version of Zea mays gff3 from EnsemblPlants, converted it to gtf with
1/27/22
Carly Graham
,
Konstantin Okonechnikov
4
1/10/22
3' Bias
Hi Carly, nope, did not work with such tools... Had another experience: combination of 2 sample
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3' Bias
Hi Carly, nope, did not work with such tools... Had another experience: combination of 2 sample
1/10/22
Barbara Binney
,
Konstantin Okonechnikov
2
1/7/22
Interpreting "Mapping quality across reference" in qualimap
Hi, Indeed mapping quality reflects possible unclear mapping due to sequence segment similarity, but
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Interpreting "Mapping quality across reference" in qualimap
Hi, Indeed mapping quality reflects possible unclear mapping due to sequence segment similarity, but
1/7/22
Esther Kockelmans
11/23/21
bamqc out of memory with 38G of java-mem-size
Hey there, I am using qualimap for analyzing an alignment I made using minimap2. Although, with every
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bamqc out of memory with 38G of java-mem-size
Hey there, I am using qualimap for analyzing an alignment I made using minimap2. Although, with every
11/23/21
xiaol...@gmail.com
,
Konstantin Okonechnikov
3
11/2/21
Qualimap RNA seq QC Reads genomic origin: further categorize the Exonic region to CDS, 5'UTR and 3'UTR
Hi, Konstantin, Thank you very much for your reply and your continuous support and improvement of
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Qualimap RNA seq QC Reads genomic origin: further categorize the Exonic region to CDS, 5'UTR and 3'UTR
Hi, Konstantin, Thank you very much for your reply and your continuous support and improvement of
11/2/21
xiaol...@gmail.com
,
Konstantin Okonechnikov
3
11/2/21
set Qualimap RAM memory usage size once instead of every-time at launch
Hi, Konstantin, Thank you very much for your help. I followed your instruction the line 7 in Qualimap
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set Qualimap RAM memory usage size once instead of every-time at launch
Hi, Konstantin, Thank you very much for your help. I followed your instruction the line 7 in Qualimap
11/2/21
Desmond
,
Konstantin Okonechnikov
2
10/15/21
Error In Setting Up in Qualimap Inside Singularity Container
HI! I suspect issue might be with Java version from OpenJDK. Did you try on earlier eg 1.7.0_79 from
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Error In Setting Up in Qualimap Inside Singularity Container
HI! I suspect issue might be with Java version from OpenJDK. Did you try on earlier eg 1.7.0_79 from
10/15/21
Alicep1! CHOURY
7/13/21
Questions about qualimap counts
Hi every body, I would like to test qualimap counts on my rnaseq data (from htseq counts) I have 2
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Questions about qualimap counts
Hi every body, I would like to test qualimap counts on my rnaseq data (from htseq counts) I have 2
7/13/21
Stephen Smith
,
Konstantin Okonechnikov
3
7/7/21
Any way to set coverage histogram max value
Hi, Just coming back to this as I've found myself using qualimap again, this time on even more
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Any way to set coverage histogram max value
Hi, Just coming back to this as I've found myself using qualimap again, this time on even more
7/7/21
Luomeng Tan
6/7/21
bamqc -gd option only has hg19 for human
Hi, I am working on a project that uses qualimap bamqc. I was wondering whether or not it would
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bamqc -gd option only has hg19 for human
Hi, I am working on a project that uses qualimap bamqc. I was wondering whether or not it would
6/7/21
Gabriel Gama
5/31/21
BAM file is empty or no read alignments are located in exonic regions.
When doing RNAseqQC, from STAR aligned transcriptome sequencing, i'm getting: code: qualimap --
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BAM file is empty or no read alignments are located in exonic regions.
When doing RNAseqQC, from STAR aligned transcriptome sequencing, i'm getting: code: qualimap --
5/31/21
Gabriel A. C. Gama
,
Konstantin Okonechnikov
5
5/31/21
Failed to run bamqc net.sf.samtools.SAMFormatException: Error parsing SAM header. @RG line missing SM tag. Line: @RG
This worked, and I got BAMqc to run just fine. Em quarta-feira, 28 de abril de 2021 às 13:51:23 UTC-3
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Failed to run bamqc net.sf.samtools.SAMFormatException: Error parsing SAM header. @RG line missing SM tag. Line: @RG
This worked, and I got BAMqc to run just fine. Em quarta-feira, 28 de abril de 2021 às 13:51:23 UTC-3
5/31/21
Mike Greenwood
,
Konstantin Okonechnikov
7
5/12/21
Not seeing Insert Size Histogram
I'm working on HLA typing and the kit we use comes with software for analysis of fastq data. The
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Not seeing Insert Size Histogram
I'm working on HLA typing and the kit we use comes with software for analysis of fastq data. The
5/12/21