9 votes
Accepted

Quantifying reads mapping to multiple loci

You almost had the correct python code already, you just need to filter out secondary alignments: ...
Devon Ryan's user avatar
  • 19.6k
8 votes
Accepted

Building STAR Genome Index for nanopore RNA sequencing

The parameter is used to determine how much sequence STAR indexes on each side of a splice junction to improve its alignment accuracy. For very long reads, this may not be ideal. I am not sure if ...
GWW's user avatar
  • 752
6 votes

STAR vs Bowtie2

What is the fundamental difference between STAR and Bowtie(2). STAR for mapping spliced (i.e. with introns) short RNA-seq reads against a genome. Bowtie2 for mapping short reads without splicing. ...
user172818's user avatar
  • 6,515
5 votes
Accepted

Is the algorithm of the STAR RNA Seq-Aligner similar to the Knuth-Morris-Pratt string matching algorithm?

No, STAR isn't using the KMP algorithm or a modification of it. The KMP algorithm is an online exact pattern matching algorithm. It does (linear time) pre-processing on the query and then finds all ...
nomad's user avatar
  • 472
5 votes

Error creating indices using STAR

Try reducing the number of threads. When multithreading the index creation (and other memory bound tasks), the memory usage increases linearly with the number of threads. If you required a 10 GiB ...
Konrad Rudolph's user avatar
5 votes
Accepted

Can I index a compressed FASTA file using STAR?

I can think of two possible workarounds. The simplest would be to try using zcat instead of gunzip -c, in case that works. ...
terdon's user avatar
  • 10.1k
5 votes
Accepted

STAR-long parameters for aligning RNA ONT reads to genome

I've had great results using minimap2, particularly when combined with a pre-treatment of Canu for error correction (using minimap2 for the read-to-read mapping): ...
gringer's user avatar
  • 14.1k
4 votes

Building STAR Genome Index for nanopore RNA sequencing

I've found the STAR manual to be incredibly helpful with trying to navigate my way round all the STAR command line parameters. Here's the section on the sjdbOverhang...
gringer's user avatar
  • 14.1k
4 votes

What process and input data is required for a cellranger reference transcriptome?

Your problem is caused by using the transcriptome fasta file rather than the genome fasta file. You've already given it transcriptome information with ...
Devon Ryan's user avatar
  • 19.6k
4 votes
Accepted

Disk space error while aligning reads using STAR

STAR versions 2.6.0b and 2.6.0a are unstable, as written Issues performing variant calling with GATK you are using version 2.6.0b. You should switch to version 2.6.0c which is stable. Also avoid to ...
bilal malik's user avatar
3 votes

Assertion `compressBound(0xff00) < 0x10000' failed when using STAR 2.7.9a

bgzf.c:158: bgzf_open: Assertion `compressBound(0xff00) < 0x10000' failed. Upstream HTSlib users encountered this problem when HTSlib was used in conjunction ...
John Marshall's user avatar
3 votes
Accepted

Error creating indices using STAR

In addition to the other answer (to reduce the number of threads), you might also need to add a --genomeChrBinNbits argument. Your reference has more than 5000 ...
benn's user avatar
  • 3,571
3 votes

STAR vs Bowtie2

The seeds are clustered together by proximity to a selected set of ‘anchor’ seeds in the 2nd phase of the STAR algorithm, but this •clustering/stitching/scoring process• is not present in Bowtie2. ...
envs_h_gang_5's user avatar
2 votes

Compare mapped reads from BWA -MEM and STAR from .bam files

Bam files contain a MAPQ field that informs on whether an alignment is unique or not. With STAR, a MAPQ value of 255 means the read is mapped uniquely and a score lower than 255 means not unique. You ...
Robert ietswaart's user avatar
2 votes
Accepted

How should I imagine the pre-indexing of suffix arrays in the STAR RNA Seq-aligner?

You can take a look at slide 40 of the lectures slides I use when I teach suffix arrays (reproduced here) An L-mer is a K-mer — STAR builds an explicit lookup table from all length 14 (by default) ...
nomad's user avatar
  • 472
2 votes

STAR aligner multiple fastq files

It seems the sequencing is single-end, and there is only one fastq per sample. If so: ...
h.mon's user avatar
  • 323
2 votes

Importance of Proper Pairs vs Aligned Reads for RNASeq data

If you check the RSeQC docs you can get an explanation of how the inner distance stats work. By the look of your inner-distance MultiQC plot I guess that your sequencing is 2x100bp reads. This plot ...
ewels's user avatar
  • 291
2 votes
Accepted

Why I am getting different gene lengths for the same genes in different samples with rsem-calculate-expression?

If there are differences in the expression of individual transcripts between samples then both the length and effective length will differ between samples. It is commonly the case that the ratio of ...
Devon Ryan's user avatar
  • 19.6k
1 vote

GTF To Use With Broad Institute Fasta In STAR

I've had success in the past generating STAR indexes using the Gencode GTF files available from here: https://www.gencodegenes.org/human/ Comprehensive gene annotation (ALL regions) Genome sequence (...
gringer's user avatar
  • 14.1k
1 vote
Accepted

GTF To Use With Broad Institute Fasta In STAR

If you are looking for a genome and its corresponding annotations, you can use the following, it is from nf-core (link to the original doc): ...
haci's user avatar
  • 4,112
1 vote

Extract mapping coverage from GTF files

So consider this, you know how many reads map to each of your genes (1). Does that tell you anything about (2) the number of reads that mapped against non-gene regions (3) the number of reads that did ...
Jvstonebridge's user avatar
1 vote
Accepted

STAR Indexing Diference for Small and Large Genome File Output

You didn't get extra information with the small genome, the index for the larger one just wasn't made. My guess is that you ran out of RAM. For mammalian sized genomes ensure you have at least 30GB of ...
Devon Ryan's user avatar
  • 19.6k
1 vote
Accepted

Importance of Proper Pairs vs Aligned Reads for RNASeq data

Differential gene analysis sees only the read counts. So the proportion of not properly paired reads will have an effect on the counts, if the programme / software used, counts fragments / read pairs ...
StupidWolf's user avatar
  • 1,688
1 vote
Accepted

Why is my STAR reference genome indexing aborting on my GNU/Linux server but not on my Mac OS X laptop?

A std::bad_alloc error tends to mean that you've run out of memory. It's not unusual for head nodes to be fairly limited in capacity, so presumably that's the issue....
Devon Ryan's user avatar
  • 19.6k

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