User: priscilladraj

gravatar for priscilladraj
Reputation:
10
Status:
New User
Location:
Last seen:
1 week, 1 day ago
Joined:
4 months, 3 weeks ago
Email:
p************@gmail.com

Posts by priscilladraj

<prev • 12 results • page 1 of 2 • next >
0
votes
1
answer
74
views
1
answers
Comment: C: filtering alignned seqeunces
... I tried this awk '{if($3 == "A.fasta") { print $0 }}' combineA_aln.sam > A_aln_reads.file wc -l A_aln_reads.file to pull out A awk '{if($3 == "B.fasta") { print $0 }}' combineB_aln.sam > B_aln_reads.file wc -l B_aln_reads.file to pull out B but its not working. Can I ...
written 8 days ago by priscilladraj10 • updated 8 days ago by lieven.sterck9.4k
1
vote
1
answer
74
views
1
answer
filtering alignned seqeunces
... Hi, I have used ONT minimap to align combined reference sequences (fasta file combined together in one file but separated by header " >" for each reference sequence). Then, I got one aligned sam file . My question is I dont know how to filter out my aligned data to each of the reference sequence. ...
alignment written 8 days ago by priscilladraj10 • updated 8 days ago by colindaven2.5k
0
votes
0
answers
156
views
0
answers
Bowtie2 or Bowtie
... Hi, I have demultiplexed reads for each of my library. So each libary contains read 1 and read 1 as I used dual indexex. Hence, I combined both reads (read 1 and read 1 specific for each pool) into one fastq.gz file. As for my reference file, I indexed the fasta file containning all my refere ...
alignment bowtie written 4 months ago by priscilladraj10 • updated 4 months ago by lieven.sterck9.4k
1
vote
2
answers
463
views
2
answers
Answer: A: filter illumina index
... thanks I manages to resolve it demultiplexing it again bcl base caller software and it worked this time because I learned that teh Iseq reads i5 from reverse complement direction. So its my mistake of not knowing this. ...
written 4 months ago by priscilladraj10
0
votes
0
answers
908
views
0
answers
Comment: C: convert multiple sequences in excel to fasta file
... yes, it did help. thanks so much. I am not sure why I count not find this earlier. thanks again :) ...
written 4 months ago by priscilladraj10
1
vote
0
answers
908
views
0
answers
(Closed) convert multiple sequences in excel to fasta file
... Hi, I have a CSV file with just two columns(ref ID and ref sequence). I would like convert this to a fasta file format so that I can align my fastq file with these reference sequences. How do I do the conversion from csv to fasta? Kindly let me know please. Thanks Pris ...
csv convert to fasta written 4 months ago by priscilladraj10
1
vote
2
answers
463
views
2
answers
filter illumina index
... Hi, I ran an iseq illumina sequencing on my libary. And due some sample prepration problem, I have a low concentration of my libary. Hence, after sequecing and base calling, the iseq base caller grouped all my reads (dual index, 3 pooled libary = 6 reads total) under a undetermined folder. I want ...
0
votes
1
answer
258
views
1
answers
Comment: C: Parse error at line.....
... Hey thanks genomax . I am still new so this small information is also useful for me :D ...
written 4 months ago by priscilladraj10
0
votes
1
answer
258
views
1
answers
Comment: C: Parse error at line.....
... hey thanks it worked :D ...
written 4 months ago by priscilladraj10
3
votes
1
answer
258
views
1
answer
Parse error at line.....
... Hi I am trying to convert sam file to bam file and encountered this problem . Not sure how to troubleshoot, Can someone help please as I am very new to bioinformatics samtools view -S -b aln2.sam > aln2.bam [W::sam_read1] Parse error at line 753646 [main_samview] truncated file. ...
alignment written 4 months ago by priscilladraj10 • updated 4 months ago by lieven.sterck9.4k

Latest awards to priscilladraj

Scholar 4 months ago, created an answer that has been accepted. For A: filter illumina index

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2065 users visited in the last hour