bijendrabio

Exclude bed format region not working!

2

Hello, I ran the EDTA with --exclude option (with --anno 1) to exclude the bed format regions from the TE annotation. However, the output file seems to contain the predicted...

run_preCluster.py --cpus=30 CalledProcessError(retcode, cmd)

1

Hello All, I am receiving following error while running the Family finding step of Cogent for a large dataset. Kindly suggest. _input file:_ isoseq_flnc.fasta _command:_ python /path/to/cDNA_Cupcake/cupcake2/tofu2/run_preCluster.py --cpus=30 raise CalledProcessError(retcode,...

TIR filtration

3

Hello Shujun, Curious if the TIR elements identified using "EDTA_raw.pl --type tir" requires filtering. Its generate two files *.intact.fa and *.raw.fa, both of which are same. Does this indicate that...

Hello, I received a following error with bedtools intersect; Could it be chromosome size limit issue? if so how can I resolve this? Kindly suggest! ``` ERROR: Received illegal bin...

gffread to protein

3

Hello, I tried to extract the coding proteins FASTA from gtf file but the output looks like the following; command used: gffread -y output_protein.fasta -g genome.fasta transcripts.gff3 output; LYT.WSHVP.QTLQSHR.CPSRLLELCSSPLLQMTIHGA.YSFGE.HIMYDIKLDNLQYVRSW.LRKLKL LVQLDKFRTCHP.TPC.SS.TSLDRLHQPAHACLWCGQQWWQYRGLVRQSQSSR.QRSYRTQLVGWREQ....

Hello, I am curious about how the liftOver tool manages to lift over genes from large inversions in a reference genome. Could you kindly provide some insights? Regards, B

tso.plot_heatmap blank plot

7

Hello, Curious if its possible to reorder the tissue samples in the heatmap? For example, if I change the order of tissues in the sample input, the heat map doesn't...

Using CDS from multiple species

1

Hello @oushujun, Just curious if using the CDS from multiple closely related species will effect the repeat annotation output? or Do you suggest removing the redundancy from he concatenated CDS...

Hello @jeffersonfparil, Wondering if it is possible to extract orthogroups or a GO term list specifically for gene family contraction/expansion results for a particular species? I found a file named...

How to visualize GO term enrichment analysis output?

2

Hello, Could you please indicate how to visualize GO term enrichment analysis output. The output generated multiple .goout files. Kindly suggest! B