Moderator: shenwei356

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shenwei3564.1k
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Posts by shenwei356

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Comment: A: How to identify contigs containing the degenerate primer sequences using python?
... (Only for full match) ``` # positive strand $ cat seqs.fa | seqkit grep -s -d -p NACTGN | seqkit seq -n -i | tee 1.txt Contig4679 Contig4682 # negative strand $ cat seqs.fa | seqkit seq -r -p | seqkit grep -s -d -p TTAM | seqkit seq -n -i | tee 2.txt Contig4681 Contig4682 # intersection $ csvtk i ...
written 8 days ago by shenwei3564.1k
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Comment: C: How to identify contigs containing the degenerate primer sequences using python?
... Partly match between PCR primer and target sequence is enough for PCR amplication. Do you still want only full match? ...
written 8 days ago by shenwei3564.1k
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Comment: C: how to reorder lines in afile based on a list of gene IDS?
... why not trying googling using keywords "r dataframe reorder factor"? ...
written 8 days ago by shenwei3564.1k
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Comment: C: how to reorder lines in afile based on a list of gene IDS?
... In R, just set the column as factor with your levels for the dataframe. For others, storing the levels in a hashmap with incremental numbers as values, then you can sort the rows using corresponding hashmap value. Want save time? [csvtk sort](https://bioinf.shenwei.me/csvtk/usage/#sort) supports s ...
written 8 days ago by shenwei3564.1k
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Comment: C: Custom nr database with only arthropods ?
... finally, there's no bug and sequences count matches (Here 6928017 ~= 6928021). ...
written 9 days ago by shenwei3564.1k
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Comment: C: Custom nr database with only arthropods ?
... test: blastp # blastdb from step 3 option 2 # time blastp -num_threads 16 -db nr.$id -query t4.fa > t4.fa.blast # real 0m20.866s # $ cat t4.fa.blast | grep Query= -A 10 # Query= A0A0J9X1W9.2 RecName: Full=Mu-theraphotoxin-Hd1a; Short=Mu-TRTX-Hd1a # # ...
written 9 days ago by shenwei3564.1k
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Answer: A: Custom nr database with only arthropods ?
... Data: - [pre-formated blastdb](ftp://ftp.ncbi.nlm.nih.gov/blast/db) (09/10/2018) - [prot.accession2taxid.gz](ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz) (09/07/2018) (optional, but recommended) Hardware in this tutorial - CPU: AMD 8-cores/16-threads 3.7Ghz - RAM: ...
written 9 days ago by shenwei3564.1k
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Comment: C: Custom nr database with only arthropods ?
... Sorry for this bug. I've downloaded the nr and rewrite the steps posted as a new answer. There's no bug now. ...
written 9 days ago by shenwei3564.1k
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Comment: C: Custom nr database with only arthropods ?
... buggy means failing to retrieve some sequences, makeblastdb works fine. option a is ouputtin from pre-built blastdb downloaded from ftp. ...
written 10 days ago by shenwei3564.1k
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Comment: C: Custom nr database with only arthropods ?
... It's the bug of the perl one-liner, because of the not well formated `nr.gz`. I gave up after few hours. May be we should blast on whole `nr` and filter the result. ...
written 10 days ago by shenwei3564.1k

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