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QualiMap

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Phillip SanMiguel, Konstantin Okonechnikov2

Dec 7

Could a minimum window size for GC (%) in "Coverage across reference" be added?

Dear Phillip, Thanks a lot for useful suggestions! I did not came across with any windows size issues

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Could a minimum window size for GC (%) in "Coverage across reference" be added?

Dear Phillip, Thanks a lot for useful suggestions! I did not came across with any windows size issues

Dec 7

hj.ga...@gmail.com, … Vita3

Nov 14

Unrecognized VM option 'MaxPermSize=1024m'

Hi, I have the same problem. This error showed up: Java memory size is set to 1200M Launching

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Unrecognized VM option 'MaxPermSize=1024m'

Hi, I have the same problem. This error showed up: Java memory size is set to 1200M Launching

Nov 14

Aurora Moreno racero

Jun 17

Coverage across reference

Hello everyone, I'm currently analyzing whole genome BAM files using both Qualimap and samtools

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Coverage across reference

Hello everyone, I'm currently analyzing whole genome BAM files using both Qualimap and samtools

Jun 17

Amy Houseman, … Konstantin Okonechnikov6

6/19/24

Combining qualimap results

Hi Heather, these input reports are generated from BAM QC mode, when it's applied with HTML

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Combining qualimap results

Hi Heather, these input reports are generated from BAM QC mode, when it's applied with HTML

6/19/24

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

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

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

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

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 Okonechnikov4

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

unread,

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 Okonechnikov3

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 Okonechnikov8

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 Okonechnikov3

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

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 Okonechnikov3

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 Clamons2

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 Okonechnikov3

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 Okonechnikov5

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 Okonechnikov3

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

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 Okonechnikov4

1/10/22

Hi Carly, nope, did not work with such tools... Had another experience: combination of 2 sample

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Hi Carly, nope, did not work with such tools... Had another experience: combination of 2 sample

1/10/22

Barbara Binney, Konstantin Okonechnikov2

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 Okonechnikov3

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 Okonechnikov3

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 Okonechnikov2

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 Okonechnikov3

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

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

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