User: fernandalpcosta

Reputation:
0
Status:
New User
Last seen:
1 day, 18 hours ago
Joined:
1 year, 10 months ago
Email:
f**************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by fernandalpcosta

<prev • 11 results • page 1 of 2 • next >
0
votes
0
answers
51
views
0
answers
Comment: C: SAVAGE is taking too long to run the haplotype reconstruction
... That's a great idea! I will try that! Thank you. ...
written 10 days ago by fernandalpcosta0
0
votes
0
answers
51
views
0
answers
Comment: C: SAVAGE is taking too long to run the haplotype reconstruction
... I'm not sure if that much coverage is necessary, but it's not unusual for virus's haplotype reconstruction. You thing that 10000x is enough? ...
written 10 days ago by fernandalpcosta0
1
vote
0
answers
51
views
0
answers
SAVAGE is taking too long to run the haplotype reconstruction
... Hello all, I'm running SAVAGE (https://bitbucket.org/jbaaijens/savage/src/master/) to get the haplotypes of a big virus (almost 3x the HIV virus' size) and it took over 72h hours to get to stage b of the SAVAGE pipeline. The sequencing has a coverage of 20000x and the reference genome has 32KB of ...
0
votes
1
answer
719
views
1
answers
Comment: C: When paired end reads doesn't join, can i consider them single-end in metagenomi
... Unfortunately is it correct, my data is really small. I ran bbduk and it only removed 6 reads from my data. Then i reran bbmerge, as expected, got no change at those 6% of merged reads. It does look like a little like a lost cause right? Should i consider it a single end reads data and continue th ...
written 8 months ago by fernandalpcosta0
0
votes
1
answer
719
views
1
answers
Comment: C: When paired end reads doesn't join, can i consider them single-end in metagenomi
... I ran bbmerge.sh today in one of my samples and got this report: ---------- BBMerge version 37.58 Writing mergable reads merged. Started output threads. Total time: 1.617 seconds. Pairs: 54443 Joined: 3442 ...
written 8 months ago by fernandalpcosta0
0
votes
1
answer
719
views
1
answers
Comment: C: When paired end reads doesn't join, can i consider them single-end in metagenomi
... Thank you for your reply Kevin. I ran FastQC with default parameters, yes. This is a real example of one of my libraries' FastQC report (just the per base sequence quality): [R1 example][1] [R2 example][2] [1]: https://ibb.co/kACtvm [2]: https://ibb.co/kDk7MR ...
written 8 months ago by fernandalpcosta0 • updated 8 months ago by genomax49k
0
votes
1
answer
719
views
1
answers
Comment: C: When paired end reads doesn't join, can i consider them single-end in metagenomi
... I'm going to try it today. As soon as i get a result, i will let you know. Thank you :) ...
written 8 months ago by fernandalpcosta0
0
votes
1
answer
719
views
1
answers
Comment: C: When paired end reads doesn't join, can i consider them single-end in metagenomi
... Another problem is that i don't have the information about the library preparation, as the size of the overlap region between R1 and R2. I used fastq-join in the default mode. According to FastQC report, i don't have adapter contamination, just a really bad score at the end of the reads. ...
written 8 months ago by fernandalpcosta0
0
votes
1
answer
719
views
1
answers
Comment: C: When paired end reads doesn't join, can i consider them single-end in metagenomi
... Thank you for your reply, i will give it a try with BBMerge on the raw reads. I tried to join the reads before trimming them, but i got less than 10% joined reads (i used fastq-join from QIIME pipeline). ...
written 8 months ago by fernandalpcosta0
2
votes
1
answer
719
views
1
answer
When paired end reads doesn't join, can i consider them single-end in metagenomic analysis?
... Hello all, I'm doing a metagenomic analysis on human samples that were sequenced by Miseq platform, paired end reads, 40 to 300pb long (it varies according to FastQC report). After the trim/quality control fase, i ended up with reads of 60 to 190 bp long, but those paired end reads aren't able to j ...
metagenomics sequencing qiime written 8 months ago by fernandalpcosta0 • updated 3 months ago by h.mon15k

Latest awards to fernandalpcosta

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 774 users visited in the last hour