Hi All,
I have recently run an ATAC-seq library on PBMCs that came back with 82% reads mapping to E.coli and only 5% mapping to the human...
9 results in 0.0021 seconds.
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Contamination of E.coli reads in ATAC-seq library
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Bam file with unmapped reads from another genome than reference
Hello everyone,
I started with bioinformatics 2 weeks ago, so maybe my question is a bit too easy for you, but I don't find any answer... -
HISAT2 unmapped reads
Hi all, I am using HISAT2 and trying to write unmapped reads from paired-end data and the flag --un is resulting in empty files. I know they are not all... -
Velvet usage
Hi everyone!
I'm trying to use velvet to work with unmapped_reads of a rna-seq experiment, to make a kind of quantification of the contaminants... -
TopHat -M/--prefilter-multihits; unmapped reads
hi!
i am confused when to use TopHat "-M/--prefilter-multihits and when not
"When mapping reads on the transcriptome,... -
How to filter paired reads that are not mapped?
Hi!,
This should be very easy but it's confusing to me. I would appreciate some help. I have paired end Illumina sequencing. I want to keep only... -
unmapped reads assigned to chromosomes
If I use samtools' "idxstats" commands, it returns information with:
1. reference sequence name (chromosome name in my case)... -
bowtie advantages over tophat
Hi everybody,
I am working of RNA-Seq data and would like to map them using bowtie and/or tophat.
I know that tophat calls... -
BWA, mostly unmapped reads
Hi all,
Hoping someone may know exactly what I did wrong off the bat here since I think we have a lot of BWA gurus here.
This is my first time...
Last edited by Michael.James.Clark; 03-02-2011, 12:45 PM.
