w****w
发帖数: 521 | |
j*p
发帖数: 411 | 2 sra 可以换bam吗？我只知道sra to fastq |
l**********1
发帖数: 5204 | 3 同意楼下的
Step one
SRAto fastq
btw LZ be careful:
cited:
The problem you are experiencing is that the version of the SRA toolkit is
out of date and that there is now an un(der)documented option in fastq-dump
to dump paired end data from an SRA-lite submission. The guidance notes on
the NCBI website you refer to are for version 2.0.1, and state that they are
not up to date:
link:
//www.biostars.org/post/show/11111/how-to-convert-sra-lite-paired-end-
submission-to-fastq/
then try
FASTQ to BAM (version 1.56.0)
by tool:
httpS//test.g2.bx.psu.edu/root?tool_id=picard_FastqToSam |
n******7
发帖数: 12463 | 4 fastq怎么可以到bam呢？
需要align啊
或者直接转成unaligned的？这个不是多此一举吗
dump
are
【在 l**********1 的大作中提到】
: 同意楼下的
: Step one
: SRAto fastq
: btw LZ be careful:
: cited:
: The problem you are experiencing is that the version of the SRA toolkit is
: out of date and that there is now an un(der)documented option in fastq-dump
: to dump paired end data from an SRA-lite submission. The guidance notes on
: the NCBI website you refer to are for version 2.0.1, and state that they are
: not up to date:
|
w****w
发帖数: 521 | 5 新的sra toolkit里已经有一个sam-dump工具,跑10G以下的小文件没什么问题，100G以
上的，跑一个2，3个礼拜还可以接受。同时跑两个，performance马上不行，要20，30
个礼拜才能完成。 |
w****w
发帖数: 521 | 6 傻了，sam-dump可以直接extract。我们感兴趣的只有几个小region,抓出来很快。不幸
的是好几个大文件都出错了。 |
j*p
发帖数: 411 | 7 still did not get LZ's point. but whatever. |
l**********1
发帖数: 5204 | 8 最新 plus 正版吗 那个soft?
Sam≂BAM format
pls refer:
What 'Picard' does?
FastqToSam converts FASTQ files to unaligned BAM files.
httPS://test.g2.bx.psu.edu/root?tool_id=picard_FastqToSam
【在 w****w 的大作中提到】
: 傻了，sam-dump可以直接extract。我们感兴趣的只有几个小region,抓出来很快。不幸
: 的是好几个大文件都出错了。
|
s******s
发帖数: 55 | 9 I think you mean cSRA to BAM? SRA to BAM 没有意义啊 |
w****w
发帖数: 521 | 10 我拿到的文件应该都是cSRA,虽然都是sra extension.
【在 s******s 的大作中提到】
: I think you mean cSRA to BAM? SRA to BAM 没有意义啊
|
w****w
发帖数: 521 | 11 原来以为只能用samtools从bam文件抽取区域，得把整个cSRA先转成bam,计算量会太大
。后来发现sam-dump有--aligned-region option,问题就解决了。
【在 j*p 的大作中提到】
: still did not get LZ's point. but whatever.
|
