User: Ric
Ric • 290
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Posts by Ric
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... Hi,
I have the following bash script:
#!/bin/bash
#usage: sh split_bam2sam-fasta_pbs.sh /path/to/reference.fasta /path/to/outputfolder/ /path/to/input/*.sorted.dedup.bam
output=$2
mkdir $output
merged=$(basename ${output})
echo $merged
#samlist=$(printf 'I="%s" ' "$ ...
written 2 hours ago by
Ric • 290
• updated
2 hours ago by
Shalu Jhanwar • 60
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... Hi, I found [orthomclToVenn][1] which allows to create venn diagramms from orthomcl results. Unfortunately,
I do not know how to create the `families.txt` (this file details which species are in which groups, first the name of the group, then the short handles that appear in groups.txt). Example:
...
written 20 days ago by
Ric • 290
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Comment:
C: Create de novo repeat library
... Are the below steps correct?
> wget -c https://www.dfam.org/releases/Dfam_3.1/families/Dfam.embl.gz
> gunzip Dfam.embl.gz
> mv Dfam.embl ${CONDA_PREFIX}/share/RepeatMasker/Libraries/
> cd ${CONDA_PREFIX}/share/RepeatMasker/Libraries/
> ../util/buildRMLibFromEMBL. ...
written 11 weeks ago by
Ric • 290
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... Thank you, is there a way or necessary to add strand information to the output of bam2hints?
**UPDATE:**
Bam2hints resutls:
> wc -l .intron-hints.gff
438503 .intron-hints.gff
.
> head .intron-hints.gff
NbV1Ch01 b2h intron 212732 212828 0 . . ...
written 3 months ago by
Ric • 290
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... Hi,
AUGUSTUS comes with a script which can filter BAM files
filterBam –uniq –paired –pairwiseAlignment –in Aligned.out.ss.bam –out Aligned.out.ssf.bam
Does StringTie does any filtering by its own or would it be possible to improve StringTie by using the above script?
Thank you in advance ...
written 3 months ago by
Ric • 290
• updated
3 months ago by
kristoffer.vittingseerup • 3.3k
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... Thank you for your link. I also found [Incorporating RNA-Seq into AUGUSTUS](http://augustus.gobics.de/binaries/readme.rnaseq.html) but they used BLAT. However, I have done all my alignment with HIsat2. Does anyone know how to change the commands to BAM files? ...
written 3 months ago by
Ric • 290
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... Hi, I ran StringTie and transdecoder. How is it possible to use these outputs as input for Augustus to predict genes with UTR?
Thank you in advance ...
written 3 months ago by
Ric • 290
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Comment:
C: Create de novo repeat library
... Thank you. I did:
> wget -c https://www.dfam.org/releases/Dfam_3.1/families/Dfam.hmm.gz
> cp Dfam.hmm ${CONDA_PREFIX}/share/RepeatMasker/Libraries
Where, can I find a free RepBase alternative for academics? Or can I anyhow create it from Dfam?
Thank you in advance,
...
written 3 months ago by
Ric • 290
0
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Comment:
C: Create de novo repeat library
... I ran `RepeatModeler -engine ncbi -database Repeats -pa 8` but I can not find `consensi.fa.classified`. Furthermore, the output folder contain the following files:
ls RM_56831.ThuMar191408352020/
consensi.fa families.stk round-1 round-2 round-3 round-4 round-5 round-6 tmpBlastXResul ...
written 3 months ago by
Ric • 290
0
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2
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235
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2
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Comment:
C: Repeats detection in a genome
... Yes, I would like to detect (de-novo) repeats in your genome. Therefore, I changed my question above. ...
written 4 months ago by
Ric • 290
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