Activity for Liguo Wang
-
Liguo Wang imported Files
-
-
-
Not sure which GTF2BED you were using. You can either download BED file directly from UCSC table browser or convert the GTF to BED using https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html
-
This issue is now fixed in CrossMap v0.3.6.
-
-
Possible fix for alt alleles mapped onto the negative strand
-
I have incorported this patch into v0.3.4 (https://sourceforge.net/projects/crossmap/files/). Please check if this version works as you expected.
-
I have incorported this patch into v0.3.4 (https://sourceforge.net/projects/crossmap/files/). Please check if this version work properly.
-
Now CrossMap (v0.3.0) supportsPython3. Use "pip3 install CrossMap" to install and test it.
-
Now CrossMap (v0.3.0) support Python3. Use "pip3 install CrossMap" to install and test it.
-
Hi, I can get your region properly mapped using your chain file. Did you use the latest version (0.2.7)? $ cat test.bed 1 64231290 64603895 $CrossMap.py BED ~/Downloads/Sorghum_bicolor_v2_to_Sorghum_bicolor_NCBIv3.chain test.bed 1 64231290 64603895 -> 1 71417887 71790492 the attached chain_to_table.py can print a chain file into a table which is more human readable.
-
The BED fie must have 12-column (standard BED format, https://genome.ucsc.edu/FAQ/FAQformat.html#format1). Otherwise, all non-standard BED lines will be skipped.
-
The BED fie must have 12-column (standard BED format, https://genome.ucsc.edu/FAQ/FAQformat.html#format1). Otherwise, all non-standard BED files will be skipped.
-
This error couldn't happen if your bed and chain files follow the specifications. Could you please provide an example?
-
RSeQC compares the "strand of reads" (after alignment) to the "strand of gene" (from your BED file) to determine if the RNA-seq experiment is strand-specific or not. Without reference genome and refernce gene model, RSeQC cann't tell if the library was prepared as strand-specific. After de novo assembly, you basicaly get mRNA sequences (partial or complete), but you still don't know which strand (+ or -) the mRNA is encoded. Liguo
-
RSeQC compares the "strand of reads" (after alignment) to the "strand of gene" (from your BED file) to determine if the RNA-seq experiment is strand-specific or not. Without reference genome and refernce gene model, RSeQC cann't tell if the library was prepared as strand-specific. After de novo assembly, you basicaly get mRNA sequences (partical or complete), but you still don't know which strand (+ or -) the mRNA is encoded. Liguo
-
RSeQC compares the "strand of reads" (after alignment) to the "strand of gene" (from your BED file) to determine if the RNA-seq experiment is strand-specific or not. Without reference genome and refernce gene model, RSeQC cann't tell if ibrary was prepared as strand-specific. After de novo assembly, you basicaly get mRNA sequences (partical or complete), but you still don't know which strand (+ or -) the mRNA is encoded. Liguo
-
HI Maria, The bed file was downloaded from UCSC table browser, I have no idea why...
-
Hi Maria, I just downloaded hg19_RefSeq.bed.gz, it contains 63169 transcripts (i.e...
-
Hi, First please make sure you use the most recent version. If the problem persists,...
-
Hi Phil, broken link has been fixed. We have no plan to support GTF as input. Most...
-
This error is issues by R when it tries to generate plot while no mismathes have...
-
Please provide more informaiotn such as which lines of code issued this error?
-
This is weird. In Python, "tab" is also considered as "space" (not vice versa).
-
This error is related to the bx-python package (https://pypi.python.org/pypi/bx-python/0.7.3...
-
This error is related to the bx-python package (https://pypi.python.org/pypi/bx-python/0.7.3...
1