Moderator: cpad0112
cpad0112 ♦ 14k
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Posts by cpad0112
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1
answer
110
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Comment:
C: Script for making exon file
... with [seqkit][1] and awk (seqkit linearizes fasta):
seqkit seq -w 0 file.fa | awk -v OFS="\n" '/^>/ {getline seq}{L=length(seq); L2=int(L/2); print $0, substr(seq,L2+1) substr(seq,1,L2) }'
output:
>ENSE00002234944
CAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGAT ...
written 3 days ago by
cpad0112 ♦ 14k
0
votes
1
answer
86
views
1
answers
Answer:
C: trimming of fasta file
... $ awk -v OFS="\n" '/^>/ {getline seq}{print $0,substr(seq,length(seq)/2-75,150)}' test.fa
>read1
CAGGTCTGGCTGGATGAAGGGCACGGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCTGCTGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCCGCCATCTGCTGGACGGCCTCCTCTCG
>read2
TTGTGAGTCA ...
written 3 days ago by
cpad0112 ♦ 14k
0
votes
3
answers
60
views
3
answers
... With [seqkit][1]:
$ seqkit grep -srip "TGTATGTAAACTTCCGACTTCAACTGTA" input.fq(.gz)
[1]: https://github.com/shenwei356/seqkit ...
written 5 days ago by
cpad0112 ♦ 14k
0
votes
2
answers
104
views
2
answers
Answer:
A: data prerprocessing coding
... library(sqldf)
input:
> data_1
id s1 s2 s3 s4
1 a 1 0 2 1
2 b 2 0 1 2
3 b 0 0 1 1
4 c 0 1 2 2
> data_2
id here
1 a a1
2 b a2
3 c a3
output:
> sqldf('select d1.*, d2."here" from data_1 as d1 join data ...
written 7 days ago by
cpad0112 ♦ 14k
0
votes
2
answers
104
views
2
answers
Comment:
C: data prerprocessing coding
... with join function:
$ join -1 1 -2 1 data1.txt data2.txt -t $'\t'
id s1 s2 s3 s4 here
a 1 0 2 1 a1
b 2 0 1 2 a2
b 0 0 1 1 a2
c 0 1 2 2 a3
with [tsv-utils][1] join function:
input:
$ cat data1.txt
id s1 s2 s3 s4
a 1 0 2 1
b 2 0 1 2
b 0 0 1 1
...
written 7 days ago by
cpad0112 ♦ 14k
0
votes
2
answers
191
views
2
answers
Answer:
C: data prerprocessing coding
... with datamash:
input:
$ cat file.txt
rowid s1 s2 s3 s4 s5
r1 0 16 15 14 4
r1 3 13 7 10 9
r1 5 11 16 5 5
r1 20 1 20 7 9
r1 15 18 1 18 7
r2 12 20 7 14 9
r2 18 0 14 20 2
r2 15 3 6 1 5
r2 20 7 5 10 0
r2 17 4 10 12 19
output:
$ datamash -sH -g ...
written 8 days ago by
cpad0112 ♦ 14k
0
votes
4
answers
202
views
4
answers
... another awk solution for flattend fasta file:
$ awk -v OFS="\n" '/^>/ {getline seq} {if ($0==">NODE_19_length_5758_cluster_19_candidate_1") print $0,seq}' test.fa
for printing sequence only:
$ awk -v OFS="\n" '/^>/ {getline seq} {if ($0==">NODE_19_length_5758_cluster_19_candid ...
written 8 days ago by
cpad0112 ♦ 14k
0
votes
4
answers
202
views
4
answers
... $ seqkit grep -w 0 -ip NODE_19_length_5758_cluster_19_candidate_1 input.fa
for printing sequence only:
$ seqkit grep -ip NODE_19_length_5758_cluster_19_candidate_1 test.fa | seqkit seq -s -w 0 ...
written 8 days ago by
cpad0112 ♦ 14k
1
vote
1
answer
152
views
1
answers
... Use fastqscreen.
1. Download the genomes of suspect organisms.
2. Index them
3. Use fastqscreen to check the contamination.
By default, fastqscreen, checks for few model genomes and contaminating vector sequences. One can supply genomes and sequences externally and check for contamination. In ...
written 15 days ago by
cpad0112 ♦ 14k
0
votes
2
answers
130
views
2
answers
... try `cutadapt` minimum length option or `seqkit seq --min-len` option ...
written 17 days ago by
cpad0112 ♦ 14k
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