Hi,
Below is a supplementary alignment for one of my reads with a mapping quality score of 43.This should map to chr2: 29446797 in hg19
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27 results in 0.0030 seconds.
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Wrong bwa alignment?
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Retrieve read IDs from SPAdes contigs
Hi everyone,
I'm using SPAdes 3.12 to assemble contigs using reads. The question is, is there any way to retrieve the reads used to assemble the... -
New to bioinformatics - Read Alignment/Mapping
Good day to you,
I am a biology b.sc. student from germany and for my graduation i am working on RNAseq data sequenced by Illumina Next... -
reads align but contigs do not??
Here is something that puzzles me:
I have 4000 reads that align to my reference genome. I can visualize them, they cover maybe 80 % or a little... -
Partitioning huge paired-end datasets with the khmer suite
The khmer suite has a workflow for partitioning reads based on graph-connectivity, which I want to test for a specific (huge) paired-end dataset.
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Number of Reads
Hi there,
I have Illumina HiSeq fastq output files. I want to know how I can find out the number of reads per sample before and after processing... -
Reason for max read length?
What exactly is it that limits the read length anyways?
Also, eventually some oligos get "out of phase" and then muddy the signal.... -
k-mers in the middle of the read
Hi All,
I'm new to RNASeq analysis and am looking for some advice on the FastQC k-mer output.
For several of my samples,... -
Sequence read (id) specific kmer frequency calculation
Hi,
How to count sequence read specific kmers from a single fasta file? I am working on Ulcerative Colitis Human Gut Microbiome data, where... -
SFF file - primers
Hello!
I am using 454 Roche Junior, I have few questions about reads of sff file.
I have splitted a SFF file into individual SFF file (according... -
how can I find a read in IGV?
Hi,
If I know the Read ID, how can i find it in integrated Genomic Viewer?
thanks! -
CNV by read_depth approach
Hey guys !
I'm actually working on a CNV project for the first time and need your help.
I mapped on a ref genome 44 Ilumina... -
Avoiding Genome Assembly: Illumina DNA-Seq in-silico Library Subtraction?
Hey all! I've got (what I consider) an interesting data processing question that I thought someone here may be able to help out with.
Study... -
Extract reads with defined nucleotide at defined aligned position
Dear all,
I would like to extract from a BAM (or SAM) file the reads that contain a specified nucleotide at a specified location. E.g.... -
[PICARD] Problems with SAM/BAM files without header
Hi there,
I have several problems when dealing with SAM/BAM files without an appropriate header inside. First of all, if there is a correct...
