xiekunwhy

Segmentation Fault when merge scallop2 gtfs

1

Hi, stringtie(v2.2.1) Segmentation Fault when I used it to merge scallop2, why? stringtie --merge -o scallop2.merge.gtf scallop2.list gtfs I used have been sent to [[email protected]](mailto:[email protected]). Best, Kun

Quickmerge before or after haplotype purging for high heter rate plant assemblies?

1

Hi, For a high heter rate (> 2%) plant genome, I got a hybrid assembly (BUSCO C ~84% D ~26%) and a ONT(~30X) alone assembly (BUSCO C ~80% D ~14%)....

Is it possible to use Bézier curve in draw.linear function

1

Hi, Is it possible to use Bézier curve in draw.linear function? Line links is so ugly. Best, Kun

Extremely long introns.

6

Hi, I found some extremly long introns in spaln results (when mapping protein sequences to genome), some are ~1Mb, is there a way to limit intron length when running splan?...

Almost all spaln mRNA without the final stop codon

6

Hi, I found that almost all spaln mRNA without the final stop codon, is there a way to include the final stop codon? here are my command lines: makeidx.pl -inp...

Would you please add doppelmark to bioconda?

3

Hi, Would you please add doppelmark to bioconda? Best, Kun

ERROR: Could not parse name

4

Hi, I got the following ERROR when using doppelmark(latest binary version) to deal with a ~210Gb bam (doppelmark --bam HX.clean.bam -output HX.dedup1.bam -parallelism 10 --clip-padding=1000 -scratch-dir tmp1 -disk-mate-shards 1000): ......

Can I use ultra to align est to references

1

Hi, Can I use ultra to align est sequences (not long reads) to references ? Best, Kun

Will this error affect final results?

1

Hi, I got the following error when running finder, will it affect the final results? fixOverlappingAndMergedTranscripts.py:347: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or...

Perform not so good for haplotype mixed assembly

21

Hi, I am trying to use HapHiC to anchor a haplotype-collapsed genome (hifiasm p_ctg), and I found that HapHiC perform not so good, **especially contig ordering,** HiC data was mapping...