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I noticed that the pipeline now has new mitochondrial read alignments. Do these alignments happen before the alignment to the nuclear genome, do they happen in parallel to the alignment for the nucle…
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Hi- I seem to be unable to make spaln work even in the most basic case. I would appreciate any guidance. This is using spaln 2.4.9 installed via bioconda. My final aim is to align proteins or cDNA fro…
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Hi,
I'm trying to combine my TACO output and TD output within this command but it returns error:
`$TD_PATH/util/cdna_alignment_orf_to_genome_orf.pl longest_orfs.cds.transdecoder.gff3 ../TACO/out…
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Hello, I have tried this pipeline and found an issue with alignment; most of the reads were not aligned. Is it possible to get the HISAT2 CHM13v2 index files? Thank you so much.
Below is the code I…
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Hi there,
Thank youf or this tool, but I am still facing the same issues as a lot of time ago.
My ATACseqQC version is 1.22.0
I am on windows 11
R=4.2.2
bioconductor=3.16.0
Am I missing someth…
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Hi Sigalign team,
Thanks for the amazing library for sequence alignment. I have a question related to aligning high similar sequences against a reference. If the read is always > some certain thre…
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Hi,
I used two mouse genomes (mm10 and GRCm39) and aligned my fastq files ( Links from Bowtie2 website: **https://genome-idx.s3.amazonaws.com/bt/mm10.zip** **and** https://genome-idx.s3.amazonaws.c…
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Hi Winnowmap Team,
I am trying to use winnowmap to do whole-genome alignments. In some cases, winnowmap is resulting in large unaligned regions like below:
 visualization, which allows to build a view of the context of a variant with the alignment between the transcript and the reference genome. It can create r…