bam-readcount returns warning

Hi, I am running bam-readcount on a bam file and getting the following warning message:

WARNING: In read WB85V:02305:02971: Couldn't find the generated tag.

What does this warning mean? The output seems to be correct otherwise.

Thanks! Tirza

software

• 3,755 views • link

updated 10.4 years ago by poisonAlien

• written 10.4 years ago by tirza.doniger •

1 answer

Yeah there was a github issue regarding this. But its safe to ignore them.

• 1 views • link

written 10.4 years ago by poisonAlien

More posts like this

bam-readcount empty output
written 4.7 years ago by D_Jens •

Hi, I am using bam-readcount. However, when I run the following input I get a blank output; $ bam-readcount -f NCBI_ReferenceGenome.fna -l decomposed.vcf Bowtie2.bam [-b …
Differential-expression analysis using logistic regression in Seurat - glm.fit warning message
written 6.8 years ago by Lucy •

Hi, I am performing differential-expression analysis in Seurat using the logistic regression test with "donor" as a latent variable. While it does give me an …
What does "-Shu" do in samtools view
written 7.0 years ago by quiocarbajal •

Hello everyone! I am getting started with chip-seq analysis so this is probably a very basic question. In the following command: samtools view -Shu s1.sam …
Warning with cuffmerge: couldn't find fasta record
written 9.0 years ago by irving.jgalo23 •

Hi im trying to run cuffmerge with my gtf anotation using the next command cuffmerge -p 8 -g TAIR_gff/TAIR10_GFF3_genes.gff -s TAIR10_chr_all_new.fa assemblies.txt But I get …
Bam-readcount output empty from certain regions (RNA seq bams)
written 9.4 years ago by nils.rudqvist •

Hi all, I am using bam-readcount to find reads in a RNA seq bam at the location of variants found using RNA seq. However, I …
what does "q2" mean in bam-readcount results?
written 9.4 years ago by gongchangzhaojie •

I found bam-readcount to be very useful for further filtering SNVs and Indels. However, I do not understand a few fields of bam-readcount outputs and …
Cufflinks- found spliced alignment without XS attribute
written 10.0 years ago by Lindsay44 •

I am getting the following command line message (various times) when running Cufflinks: **BAM record error: found spliced alignment without XS attribute** What does this …
Could not find fasta record: CuffCompare & Cuffmerge
written 10.2 years ago by EpiExplorer

Hi , I am using the genes.gtf and genome.fa files from iGenomes for Homo sapiens Ensemble GRCh37, for cuffcompare and cuffmerge. But I get the …
bam- readcount error
written 10.2 years ago by mark.rose •

When running bam-readcount I get (minus the 8M previous warnings of the same type): WARNING: In read m151222_205817_42179_c100908792550000001823210904291644_s1_p0/4606/0_7297: Couldn't find the generated tag. WARNING: In …
How To Fix A Bam-Readcount Sm Error: "Couldn'T Grab Single-End Mapping Quality For Read"
written 13.3 years ago by amnonim •

<p>Hi I'm using <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a>-readcount to get coverage per nucleotide as part of our exome-seq variant annotation pipeline, following <a href='http://bio-bwa.sourceforge.net/'>bwa</a> and gatk when i …