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I'm trying to map some PacBio IsoSeq data (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97785) to compare versus my own data generated by Illumina and other platforms.
minimap2-2.7_x64-lin…
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Dear Florian G. Pflug and Arndt von Haeseler,
I found your paper https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty283/4972993 and find it very interesting and u…
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Hi Heng,
I just used minimap2 (version 2.2) for spliced alignment of PacBio reads to human genome.
I used “-ax splice” option.
For some reason, the minimap2 output alignments do not contain s…
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Great project!
Are there any plans to support chimeric alignment (similar to GMAP) in addition to spliced long-sequence alignment? This would be great, as GMAP (and to some extent STAR) is to my kn…
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Hi,
I want to use STAR to map some large Illumina RNA datasets (98bp, 400-600mio, single-end) to a quite repetitive "transcriptome".
The reference contains ~3mio sequences, ranging from 100bp to …
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Hi
I am currently trying to get pasa working, however I can't seem to get it to work on the sample data. Could you please let me know what might be causing the issue (gmap/2017-09-30 , BLAT/36, pa…
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Hi IUC-Team!
The current hisat2-wrapper doesn't check for paired-end input in the "Spliced alignment parameters"-section and can generate wrong output when the option --rna-strandness is used.
Acc…
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I have tried to use gffread-0.9.9.Linux_x86_64 to merge EnsEMBL and RefSeq GTF annotations
with adjusted chromosome naming.
Program call:
cat GRCm38.RefSeqwoChrSlimmed.gtf GRCm38.87_slimmed.gtf…
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Hello,
I am running StringTie for sorted, merged bam files with both guided (-G) and unguided option. Interestingly, I can't get the process done for unstranded bam file (the size is around 260 GB;…
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I see a few posts on GMAP versions (https://github.com/PASApipeline/PASApipeline/issues/35 and https://github.com/PASApipeline/PASApipeline/issues/31) and updating PASA to deal with those changes. I …